SUPERFAMILY 1.75 HMM library and genome assignments server

SMAD MH1 domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   SMAD MH1 domain [ 56365]
Superfamily:   SMAD MH1 domain [ 56366]
Families:   SMAD MH1 domain [ 56367]


Superfamily statistics
Genomes (139) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,175 1,320 2
Proteins 1,168 1,317 2


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) developmental process 0 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0 Least Informative Direct
Biological Process (BP) multicellular organismal process 0 Least Informative Direct
Biological Process (BP) response to stimulus 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.000003004 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 0.0328 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.03376 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.01578 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.009869 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.9266 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.8714 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.01737 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.8984 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.8889 Least Informative Inherited
Biological Process (BP) cell differentiation 0 Moderately Informative Direct
Biological Process (BP) signal transduction 0 Moderately Informative Direct
Biological Process (BP) response to endogenous stimulus 0.0000000000004401 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.00000000001135 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.00000000282 Moderately Informative Direct
Biological Process (BP) reproductive process 0.00000002585 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.00000003095 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.000000255 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.0000003944 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.0000004366 Moderately Informative Direct
Biological Process (BP) tissue development 0.000005143 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.000008713 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.00001728 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.0004193 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.0005678 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0.0006195 Moderately Informative Direct
Biological Process (BP) immune system process 0.0007901 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.006328 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.02425 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.04116 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.195 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.2462 Moderately Informative Inherited
Biological Process (BP) regulation of phosphorus metabolic process 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.02535 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.04295 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.3464 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.6578 Moderately Informative Inherited
Biological Process (BP) organ development 0.08251 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.04357 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.2816 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.04346 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.2297 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.08358 Moderately Informative Inherited
Biological Process (BP) gene expression 0.3163 Moderately Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 0 Informative Direct
Biological Process (BP) growth 0.00000000000009765 Informative Direct
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.00000000001443 Informative Direct
Biological Process (BP) locomotion 0.0000000002517 Informative Direct
Biological Process (BP) cardiovascular system development 0.0000000007921 Informative Direct
Biological Process (BP) tissue morphogenesis 0.000000001021 Informative Direct
Biological Process (BP) generation of neurons 0.000000002474 Informative Direct
Biological Process (BP) embryonic morphogenesis 0.00000002575 Informative Direct
Biological Process (BP) cell proliferation 0.00000002693 Informative Direct
Biological Process (BP) phosphorylation 0.0000000327 Informative Direct
Biological Process (BP) tube development 0.0000001163 Informative Direct
Biological Process (BP) positive regulation of developmental process 0.000006523 Informative Direct
Biological Process (BP) positive regulation of multicellular organismal process 0.000006823 Informative Direct
Biological Process (BP) cell projection organization 0.00001501 Informative Direct
Biological Process (BP) cellular component movement 0.00002591 Informative Direct
Biological Process (BP) cellular process involved in reproduction in multicellular organism 0.0000595 Informative Direct
Biological Process (BP) organ morphogenesis 0.0001659 Informative Direct
Biological Process (BP) regulation of growth 0.0002807 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.0004801 Informative Direct
Biological Process (BP) transcription, DNA-templated 0.0005016 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.004421 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.7685 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.6557 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.7084 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.7599 Informative Inherited
Biological Process (BP) synaptic transmission 0.3964 Informative Inherited
Biological Process (BP) gland development 0.01666 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 1 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.01428 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.4477 Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 0.001006 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.009566 Informative Inherited
Biological Process (BP) central nervous system development 0.694 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.001011 Informative Inherited
Biological Process (BP) cell division 0.02165 Informative Inherited
Biological Process (BP) single organism reproductive process 0.001526 Informative Inherited
Biological Process (BP) sexual reproduction 0.001816 Informative Inherited
Biological Process (BP) sensory organ development 0.6578 Informative Inherited
Biological Process (BP) epithelium development 0.01218 Informative Inherited
Biological Process (BP) embryonic organ development 0.01482 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.006694 Informative Inherited
Biological Process (BP) pattern specification process 0 Highly Informative Direct
Biological Process (BP) regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 0 Highly Informative Direct
Biological Process (BP) cellular response to growth factor stimulus 0 Highly Informative Direct
Biological Process (BP) regulation of binding 0 Highly Informative Direct
Biological Process (BP) in utero embryonic development 0.000000000000009016 Highly Informative Direct
Biological Process (BP) neuron projection development 0.0000000000005412 Highly Informative Direct
Biological Process (BP) cell projection morphogenesis 0.0000000000008439 Highly Informative Direct
Biological Process (BP) mesenchyme development 0.00000000001272 Highly Informative Direct
Biological Process (BP) regulation of cellular response to growth factor stimulus 0.00000000003569 Highly Informative Direct
Biological Process (BP) skeletal system development 0.000000006456 Highly Informative Direct
Biological Process (BP) ossification 0.00000005824 Highly Informative Direct
Biological Process (BP) protein phosphorylation 0.00000009865 Highly Informative Direct
Biological Process (BP) cell fate commitment 0.0000003853 Highly Informative Direct
Biological Process (BP) developmental growth 0.0000004151 Highly Informative Direct
Biological Process (BP) kidney development 0.0000023 Highly Informative Direct
Biological Process (BP) post-embryonic development 0.000003229 Highly Informative Direct
Biological Process (BP) regulation of organ morphogenesis 0.00002432 Highly Informative Direct
Biological Process (BP) stem cell development 0.00002577 Highly Informative Direct
Biological Process (BP) positive regulation of growth 0.00002603 Highly Informative Direct
Biological Process (BP) transcription from RNA polymerase II promoter 0.00005136 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 0.00005708 Highly Informative Direct
Biological Process (BP) chemotaxis 0.00009894 Highly Informative Direct
Biological Process (BP) post-embryonic organ development 0.0003132 Highly Informative Direct
Biological Process (BP) positive regulation of cellular component biogenesis 0.002175 Highly Informative Inherited
Biological Process (BP) connective tissue development 0.01752 Highly Informative Inherited
Biological Process (BP) embryonic organ morphogenesis 0.08507 Highly Informative Inherited
Biological Process (BP) regulation of developmental growth 0.002745 Highly Informative Inherited
Biological Process (BP) germ cell development 0.007671 Highly Informative Inherited
Biological Process (BP) endocrine system development 0.002021 Highly Informative Inherited
Biological Process (BP) epithelial cell development 0.01402 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.2244 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.00965 Highly Informative Inherited
Biological Process (BP) columnar/cuboidal epithelial cell differentiation 0.03602 Highly Informative Inherited
Biological Process (BP) heart morphogenesis 0.04135 Highly Informative Inherited
Biological Process (BP) branching morphogenesis of an epithelial tube 1 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) nucleic acid binding transcription factor activity 0.0000000000008048 Informative Direct
Molecular Function (MF) chromatin binding 0.0000000000008288 Informative Direct
Molecular Function (MF) molecular transducer activity 0.00000000008625 Informative Direct
Molecular Function (MF) protein complex binding 0.00009754 Informative Direct
Molecular Function (MF) transcription factor binding 0.0001314 Highly Informative Direct
Molecular Function (MF) structure-specific DNA binding 0.004938 Highly Informative Inherited
Molecular Function (MF) sequence-specific DNA binding 0.3252 Highly Informative Inherited
Molecular Function (MF) transcription regulatory region DNA binding 1 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.00000000000006252 Least Informative Direct
Cellular Component (CC) protein complex 0.000007677 Least Informative Direct

Document: GO annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0Least InformativeDirect
Disease Ontology (DO)immune system disease0.1804Least InformativeInherited
Disease Ontology (DO)urinary system disease0.001737Moderately InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.009425Moderately InformativeInherited
Disease Ontology (DO)connective tissue disease0.0266Moderately InformativeInherited
Disease Ontology (DO)glomerulonephritis0.0000007011InformativeDirect
Disease Ontology (DO)rheumatic disease0.00008696InformativeDirect
Disease Ontology (DO)collagen disease0.0001075InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Mode of Inheritance (MI)Autosomal dominant inheritance0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of cardiac morphology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the vasculature0Moderately InformativeDirect
Phenotypic Abnormality (PA)Generalized abnormality of skin0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the systemic arterial tree0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of cardiovascular system physiology0InformativeDirect
Phenotypic Abnormality (PA)Vascular skin abnormality0InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cardiovascular system phenotype0Least InformativeDirect
Mammalian Phenotype (MP)mortality/aging0Least InformativeDirect
Mammalian Phenotype (MP)abnormal homeostasis0.01516Least InformativeInherited
Mammalian Phenotype (MP)growth/size/body phenotype0.02233Least InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal cardiovascular development0Moderately InformativeDirect
Mammalian Phenotype (MP)preweaning lethality0Moderately InformativeDirect
Mammalian Phenotype (MP)muscle phenotype0.0001241Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal reproductive system physiology0.0001986Moderately InformativeDirect
Mammalian Phenotype (MP)tumorigenesis0.0003461Moderately InformativeDirect
Mammalian Phenotype (MP)digestive/alimentary phenotype0.001587Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hormone level0.03793Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system morphology0.1709Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.1741Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal craniofacial morphology1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal embryogenesis/ development1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal craniofacial development0.000003578InformativeDirect
Mammalian Phenotype (MP)increased malignant tumor incidence0.000004129InformativeDirect
Mammalian Phenotype (MP)abnormal fertility/fecundity0.00009046InformativeDirect
Mammalian Phenotype (MP)embryonic lethality0.005676InformativeInherited
Mammalian Phenotype (MP)abnormal prenatal growth/weight/body size0.00747InformativeInherited
Mammalian Phenotype (MP)abnormal pituitary hormone level0.02206InformativeInherited
Mammalian Phenotype (MP)abnormal developmental patterning0.0568InformativeInherited
Mammalian Phenotype (MP)abnormal extraembryonic tissue morphology0.162InformativeInherited
Mammalian Phenotype (MP)decreased germ cell number0.4223InformativeInherited
Mammalian Phenotype (MP)abnormal heart ventricle morphology0.7204InformativeInherited
Mammalian Phenotype (MP)hemorrhage0.8789InformativeInherited
Mammalian Phenotype (MP)increased gonad tumor incidence0.0000000001311Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mesoderm development0.000003772Highly InformativeDirect
Mammalian Phenotype (MP)abnormal follicle stimulating hormone level0.0000195Highly InformativeDirect
Mammalian Phenotype (MP)premature aging0.00005957Highly InformativeDirect
Mammalian Phenotype (MP)decreased litter size0.00007524Highly InformativeDirect
Mammalian Phenotype (MP)abnormal embryonic growth/weight/body size0.0003075Highly InformativeDirect
Mammalian Phenotype (MP)embryonic lethality during organogenesis0.0004335Highly InformativeDirect
Mammalian Phenotype (MP)ventricular septal defect0.0005344Highly InformativeDirect
Mammalian Phenotype (MP)internal hemorrhage0.001872Highly InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system development0.005528Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism environmental stimulus response variant0.00008212Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.00193Least InformativeInherited
Worm Phenotype (WP)pericellular component development variant0.00003469Moderately InformativeDirect
Worm Phenotype (WP)organism segment morphology variant0.002327Moderately InformativeInherited
Worm Phenotype (WP)organ system development variant0.005766Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.5049Moderately InformativeInherited
Worm Phenotype (WP)sensillum morphology variant0.000000003069InformativeDirect
Worm Phenotype (WP)transgene expression reduced0.0000006374InformativeDirect
Worm Phenotype (WP)male morphology variant0.0000009891InformativeDirect
Worm Phenotype (WP)body length variant0.0004989InformativeDirect
Worm Phenotype (WP)body width variant0.000607InformativeDirect
Worm Phenotype (WP)male tail morphology variant0.00000003424Highly InformativeDirect
Worm Phenotype (WP)cuticle development variant0.00000003424Highly InformativeDirect
Worm Phenotype (WP)male nervous system morphology variant0.0000001187Highly InformativeDirect
Worm Phenotype (WP)nervous system development variant0.000002445Highly InformativeDirect
Worm Phenotype (WP)dauer development variant0.000006988Highly InformativeDirect
Worm Phenotype (WP)dauer arrest variant0.00001654Highly InformativeDirect
Worm Phenotype (WP)small0.00002192Highly InformativeDirect
Worm Phenotype (WP)germline proliferation variant0.00002454Highly InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0Least InformativeDirect
Fly Phenotype (FP)neuroanatomy defective0Moderately InformativeDirect
Fly Phenotype (FP)mitotic cell cycle defective0InformativeDirect
Fly Phenotype (FP)size defective0.0007051InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)larva0Least InformativeDirect
Fly Anatomy (FA)adult0Least InformativeDirect
Fly Anatomy (FA)organ system0Least InformativeDirect
Fly Anatomy (FA)cell0Least InformativeDirect
Fly Anatomy (FA)multi-tissue structure0Least InformativeDirect
Fly Anatomy (FA)organ system subdivision0Least InformativeDirect
Fly Anatomy (FA)anatomical group0.2017Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)thoracic segment0Moderately InformativeDirect
Fly Anatomy (FA)adult segment0Moderately InformativeDirect
Fly Anatomy (FA)adult thorax0Moderately InformativeDirect
Fly Anatomy (FA)peripheral nervous system0Moderately InformativeDirect
Fly Anatomy (FA)neuron0Moderately InformativeDirect
Fly Anatomy (FA)late embryo0Moderately InformativeDirect
Fly Anatomy (FA)adult integumentary system0Moderately InformativeDirect
Fly Anatomy (FA)appendage0Moderately InformativeDirect
Fly Anatomy (FA)developing material anatomical entity0Moderately InformativeDirect
Fly Anatomy (FA)tagmatic subdivision of integument0Moderately InformativeDirect
Fly Anatomy (FA)multi-cell-component structure0.00824Moderately InformativeInherited
Fly Anatomy (FA)reproductive system0.04287Moderately InformativeInherited
Fly Anatomy (FA)central nervous system0.08436Moderately InformativeInherited
Fly Anatomy (FA)prepupa0InformativeDirect
Fly Anatomy (FA)pupa0InformativeDirect
Fly Anatomy (FA)imaginal precursor0InformativeDirect
Fly Anatomy (FA)germline stem cell0.000007168InformativeDirect
Fly Anatomy (FA)labral segment0.001029InformativeInherited
Fly Anatomy (FA)synaptic neuropil0.001205InformativeInherited
Fly Anatomy (FA)neuromere0.001222InformativeInherited
Fly Anatomy (FA)alimentary canal0.003882InformativeInherited
Fly Anatomy (FA)cell component0.008441InformativeInherited
Fly Anatomy (FA)ovariole0.008591InformativeInherited
Fly Anatomy (FA)embryonic/larval digestive system0.009796InformativeInherited
Fly Anatomy (FA)wing disc0Highly InformativeDirect
Fly Anatomy (FA)female germline stem cell0.000001798Highly InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0.6095Least InformativeInherited
Xenopus ANatomical entity (XAN)multi-tissue structure0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)embryonic structure0.004126Moderately InformativeInherited
Xenopus ANatomical entity (XAN)visual system0.2379Moderately InformativeInherited
Xenopus ANatomical entity (XAN)notochord0.00022InformativeDirect
Xenopus ANatomical entity (XAN)endoderm0.0007509InformativeDirect
Xenopus ANatomical entity (XAN)anatomical direction0.001644InformativeInherited
Xenopus ANatomical entity (XAN)pharyngeal region0.003754InformativeInherited
Xenopus ANatomical entity (XAN)primordium0.01915InformativeInherited
Xenopus ANatomical entity (XAN)heart0.05793InformativeInherited
Xenopus ANatomical entity (XAN)eye primordium0.00001356Highly InformativeDirect

Document: XA annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentCytoplasm0.000000113Least InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationDevelopmental protein0.00001772Moderately InformativeDirect
Post-translational modificationAcetylation0.00000000001744Least InformativeDirect
Post-translational modificationPhosphoprotein0.00000001261Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0.00000000004591Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR013019 SSF56366 Protein matches
Abstract

Smad proteins are signal transducers and transcriptional comodulators of the TGF-beta superfamily of ligands, which play a central role in regulating a broad range of cellular responses, including cell growth, differentiation, and specification of developmental fate, in diverse organisms from C. elegans to humans. Ligand binding to specific transmembrane receptor kinases induces receptor oligomerization and phosphorylation of the receptor specific Smad protein (R-Smad) in the cytoplasm. The R-Smad proteins regulate distinct signaling pathways. Smad1, 5 and 8 mediate the signals of bone morphogenetic proteins (BMPs), while Smad2 and 3 mediate the signals of activins and TGF-betas. Upon ligand stimulation, R-Smad proteins are phosphorylated at the conserved C-terminal tail sequence, SS*xS* (where S* denotes a site of phosphorylation). The phosphorylated states of R-Smad proteins form heteromeric complexes with Smad4 and are translocated into the nucleus. In the nucleus, the heteromeric complexes function as gene-specific transcription activators by binding to promoters and interacting with transcriptional coactivators. Smad6 and Smad7 are inhibitory Smad proteins that inhibit TGF-beta signaling by interfering with either receptor-mediated phosphorylation or hetero-oligomerization between Smad4 and R-Smad proteins. Smad proteins comprise two conserved MAD homology domains, one in the N-terminus (MH1) and one in the C-terminus (MH2), separated by a more variable, proline-rich linker region. The MH1 domain has a role in DNA binding and negatively regulates the functions of MH2 domain, whereas the MH2 domain is responsible for transactivation and mediates phosphorylation-triggered heteromeric assembly between Smad4 and R-Smad [PubMed9741623, PubMed11779503].

The MH1 domain adopts a compact globular fold, with four alpha helices, six short beta strands, and five loops. The N-terminal half of the sequence consists of three alpha helices, and the C-terminal half contains all six beta strands, which form two small beta sheets and one beta hairpin. The fourth alpha helix is located in the hydrophobic core of the molecule, surrounded by the N-terminal three alpha helices on one side and by the two small beta sheets and the beta hairpin on the other side. These secondary structural elements are connected with five intervening surface loops. The MH1 domain employs a novel DNA-binding motif, an 11-residue beta-hairpin formed by strands B2 and B3, to contact DNA in the major groove. Two residues in the L3 loop and immediately preceding strand B2 also contribute significantly to DNA recognition. The beta hairpin appears to protrude outward from the globular MH1 core [PubMed9741623].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 1 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a SMAD MH1 domain domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 1 hidden Markov models representing the SMAD MH1 domain superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) · Internal database links ]