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) multicellular organismal process 0 Least Informative Direct
Biological Process (BP) response to stimulus 0 Least Informative Direct
Biological Process (BP) regulation of metabolic process 2.298e-14 Least Informative Direct
Biological Process (BP) single-organism cellular process 1.689e-09 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.01023 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.7993 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.8293 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.8639 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.899 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.006548 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.01498 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.02803 Least Informative Inherited
Biological Process (BP) signal transduction 0 Moderately Informative Direct
Biological Process (BP) cell differentiation 0 Moderately Informative Direct
Biological Process (BP) response to endogenous stimulus 3.517e-13 Moderately Informative Direct
Biological Process (BP) regulation of biosynthetic process 6.049e-12 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1.588e-07 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 1.614e-07 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 3.072e-07 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 3.679e-07 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 4.788e-06 Moderately Informative Direct
Biological Process (BP) response to organic substance 6.601e-06 Moderately Informative Direct
Biological Process (BP) reproduction 1.573e-05 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.0003698 Moderately Informative Direct
Biological Process (BP) immune system process 0.0007389 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0.0009323 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.02393 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.02571 Moderately Informative Inherited
Biological Process (BP) organ development 0.3138 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.1653 Moderately Informative Inherited
Biological Process (BP) tissue development 0.006812 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.01139 Moderately Informative Inherited
Biological Process (BP) regulation of phosphate metabolic process 0.001022 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.03415 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.03478 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.03494 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.06952 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.01152 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.143 Moderately Informative Inherited
Biological Process (BP) system process 0.7459 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.2783 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.2317 Moderately Informative Inherited
Biological Process (BP) gene expression 0.2817 Moderately Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 0 Informative Direct
Biological Process (BP) growth 6.409e-14 Informative Direct
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 7.308e-12 Informative Direct
Biological Process (BP) cardiovascular system development 8.941e-11 Informative Direct
Biological Process (BP) locomotion 2.244e-10 Informative Direct
Biological Process (BP) generation of neurons 2.045e-09 Informative Direct
Biological Process (BP) tube development 2.256e-09 Informative Direct
Biological Process (BP) tissue morphogenesis 6.214e-09 Informative Direct
Biological Process (BP) phosphorylation 4.175e-08 Informative Direct
Biological Process (BP) embryonic morphogenesis 2.495e-07 Informative Direct
Biological Process (BP) cellular response to endogenous stimulus 5.106e-07 Informative Direct
Biological Process (BP) positive regulation of developmental process 3.497e-06 Informative Direct
Biological Process (BP) cell projection organization 0.0001113 Informative Direct
Biological Process (BP) cellular component movement 0.000182 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.0002954 Informative Direct
Biological Process (BP) regulation of growth 0.0003398 Informative Direct
Biological Process (BP) transcription, DNA-dependent 0.0004728 Informative Direct
Biological Process (BP) negative regulation of developmental process 0.0005294 Informative Direct
Biological Process (BP) sexual reproduction 0.0005442 Informative Direct
Biological Process (BP) multicellular organismal reproductive process 0.000642 Informative Direct
Biological Process (BP) organ morphogenesis 0.0007129 Informative Direct
Biological Process (BP) single organism reproductive process 0.0008396 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 0.4803 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.6234 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.5237 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.5849 Informative Inherited
Biological Process (BP) sensory organ development 0.79 Informative Inherited
Biological Process (BP) synaptic transmission 0.1692 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.005984 Informative Inherited
Biological Process (BP) gland development 0.004662 Informative Inherited
Biological Process (BP) embryonic organ development 0.02686 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.02513 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.01331 Informative Inherited
Biological Process (BP) cellular process involved in reproduction 0.001406 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.4874 Informative Inherited
Biological Process (BP) central nervous system development 0.5649 Informative Inherited
Biological Process (BP) muscle tissue development 0.7536 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.7476 Informative Inherited
Biological Process (BP) regulation of cell development 0.5022 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 1 Informative Inherited
Biological Process (BP) epithelium development 0.3458 Informative Inherited
Biological Process (BP) regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 0 Highly Informative Direct
Biological Process (BP) regulation of striated muscle tissue development 0 Highly Informative Direct
Biological Process (BP) regulation of binding 0 Highly Informative Direct
Biological Process (BP) pattern specification process 0 Highly Informative Direct
Biological Process (BP) cellular response to growth factor stimulus 0 Highly Informative Direct
Biological Process (BP) axon development 1.944e-15 Highly Informative Direct
Biological Process (BP) cell morphogenesis involved in neuron differentiation 1.091e-14 Highly Informative Direct
Biological Process (BP) cell projection morphogenesis 6.615e-13 Highly Informative Direct
Biological Process (BP) regulation of cellular response to growth factor stimulus 3.583e-11 Highly Informative Direct
Biological Process (BP) renal system development 1.552e-10 Highly Informative Direct
Biological Process (BP) skeletal system development 1.669e-09 Highly Informative Direct
Biological Process (BP) protein phosphorylation 1.719e-09 Highly Informative Direct
Biological Process (BP) ossification 3.286e-08 Highly Informative Direct
Biological Process (BP) cell fate commitment 5.539e-07 Highly Informative Direct
Biological Process (BP) developmental growth 1.995e-06 Highly Informative Direct
Biological Process (BP) post-embryonic development 2.103e-06 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 1.168e-05 Highly Informative Direct
Biological Process (BP) positive regulation of growth 1.771e-05 Highly Informative Direct
Biological Process (BP) regulation of organ morphogenesis 2.595e-05 Highly Informative Direct
Biological Process (BP) stem cell development 3.41e-05 Highly Informative Direct
Biological Process (BP) transcription from RNA polymerase II promoter 4.836e-05 Highly Informative Direct
Biological Process (BP) chemotaxis 0.0001207 Highly Informative Direct
Biological Process (BP) cellular process involved in reproduction in multicellular organism 0.0005108 Highly Informative Direct
Biological Process (BP) cell division 0.0005433 Highly Informative Direct
Biological Process (BP) post-embryonic organ development 0.0007699 Highly Informative Direct
Biological Process (BP) connective tissue development 0.003782 Highly Informative Inherited
Biological Process (BP) embryonic organ morphogenesis 0.08795 Highly Informative Inherited
Biological Process (BP) regulation of developmental growth 0.002859 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.2245 Highly Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 0.007625 Highly Informative Inherited
Biological Process (BP) endocrine system development 0.001442 Highly Informative Inherited
Biological Process (BP) mesenchyme development 0.02434 Highly Informative Inherited
Biological Process (BP) limb morphogenesis 0.1039 Highly Informative Inherited
Biological Process (BP) heart morphogenesis 0.04231 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 9.094e-13 Informative Direct
Molecular Function (MF) chromatin binding 6.925e-11 Informative Direct
Molecular Function (MF) molecular transducer activity 0.0002443 Informative Direct
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 4.09e-14 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0.0001382 Highly Informative Direct
Molecular Function (MF) structure-specific DNA binding 0.0189 Highly Informative Inherited
Molecular Function (MF) transcription regulatory region DNA binding 0.9897 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 3.201e-14 Least Informative Direct
Cellular Component (CC) protein complex 7.328e-06 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.6518 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 5.694e-09 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.1398 Moderately Informative Inherited
Cellular Component (CC) nucleoplasm part 9.601e-05 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 disease0.1862Least InformativeInherited
Disease Ontology (DO)urinary system disease0.001731Moderately InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.01662Moderately InformativeInherited
Disease Ontology (DO)nephritis9.743e-06InformativeDirect
Disease Ontology (DO)rheumatic disease0.0001554InformativeDirect
Disease Ontology (DO)collagen disease0.0001932InformativeDirect

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 the vasculature0Moderately InformativeDirect
Phenotypic Abnormality (PA)Generalized abnormality of skin0.04212Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the systemic arterial tree0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the aortic valve2.018e-05InformativeDirect
Phenotypic Abnormality (PA)Vascular skin abnormality0.0009041InformativeDirect

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 homeostasis0.01486Least InformativeInherited
Mammalian Phenotype (MP)growth/size/body phenotype0.02223Least 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 phenotype0.0001185Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal tumor incidence0.0001971Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal reproductive system physiology0.0002023Moderately InformativeDirect
Mammalian Phenotype (MP)digestive/alimentary phenotype0.01295Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hormone level0.03692Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.1699Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system morphology0.173Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal craniofacial morphology1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal embryogenesis/ development1Moderately InformativeInherited
Mammalian Phenotype (MP)increased malignant tumor incidence3.777e-06InformativeDirect
Mammalian Phenotype (MP)abnormal fertility/fecundity9.312e-05InformativeDirect
Mammalian Phenotype (MP)abnormal craniofacial development0.0001235InformativeDirect
Mammalian Phenotype (MP)embryonic lethality0.005511InformativeInherited
Mammalian Phenotype (MP)abnormal prenatal growth/weight/body size0.007402InformativeInherited
Mammalian Phenotype (MP)abnormal developmental patterning0.01992InformativeInherited
Mammalian Phenotype (MP)abnormal pituitary hormone level0.02247InformativeInherited
Mammalian Phenotype (MP)abnormal placenta morphology0.2447InformativeInherited
Mammalian Phenotype (MP)abnormal heart septum morphology0.2829InformativeInherited
Mammalian Phenotype (MP)decreased germ cell number0.4249InformativeInherited
Mammalian Phenotype (MP)abnormal heart ventricle morphology0.709InformativeInherited
Mammalian Phenotype (MP)hemorrhage0.8795InformativeInherited
Mammalian Phenotype (MP)increased gonad tumor incidence1.054e-10Highly InformativeDirect
Mammalian Phenotype (MP)absent primordial germ cells6.27e-09Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mesoderm development3.825e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal follicle stimulating hormone level1.864e-05Highly InformativeDirect
Mammalian Phenotype (MP)premature aging6.032e-05Highly InformativeDirect
Mammalian Phenotype (MP)decreased litter size7.982e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal embryonic growth/weight/body size0.0003055Highly InformativeDirect
Mammalian Phenotype (MP)embryonic lethality during organogenesis0.0004245Highly InformativeDirect
Mammalian Phenotype (MP)ventricular septal defect0.0004993Highly InformativeDirect
Mammalian Phenotype (MP)abnormal digestive system development0.001777Highly InformativeInherited
Mammalian Phenotype (MP)internal hemorrhage0.001829Highly 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 variant8.212e-05Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.00193Least InformativeInherited
Worm Phenotype (WP)pericellular component development variant3.469e-05Moderately 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 variant3.069e-09InformativeDirect
Worm Phenotype (WP)transgene expression reduced6.374e-07InformativeDirect
Worm Phenotype (WP)male morphology variant9.891e-07InformativeDirect
Worm Phenotype (WP)body length variant0.0004989InformativeDirect
Worm Phenotype (WP)body width variant0.000607InformativeDirect
Worm Phenotype (WP)male tail morphology variant3.424e-08Highly InformativeDirect
Worm Phenotype (WP)cuticle development variant3.424e-08Highly InformativeDirect
Worm Phenotype (WP)male nervous system morphology variant1.187e-07Highly InformativeDirect
Worm Phenotype (WP)nervous system development variant2.445e-06Highly InformativeDirect
Worm Phenotype (WP)dauer development variant6.988e-06Highly InformativeDirect
Worm Phenotype (WP)dauer arrest variant1.654e-05Highly InformativeDirect
Worm Phenotype (WP)small2.192e-05Highly InformativeDirect
Worm Phenotype (WP)germline proliferation variant2.454e-05Highly 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 defective0.0007043InformativeDirect

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)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 group0.2069Least 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 structure0.008158Moderately InformativeInherited
Fly Anatomy (FA)reproductive system0.04383Moderately InformativeInherited
Fly Anatomy (FA)central nervous system0.08588Moderately InformativeInherited
Fly Anatomy (FA)head0.4146Moderately InformativeInherited
Fly Anatomy (FA)prepupa0InformativeDirect
Fly Anatomy (FA)pupa0InformativeDirect
Fly Anatomy (FA)imaginal precursor0InformativeDirect
Fly Anatomy (FA)germline stem cell7.185e-06InformativeDirect
Fly Anatomy (FA)labral segment0.001041InformativeInherited
Fly Anatomy (FA)synaptic neuropil0.001181InformativeInherited
Fly Anatomy (FA)neuromere0.001231InformativeInherited
Fly Anatomy (FA)digestive system0.007885InformativeInherited
Fly Anatomy (FA)ovariole0.008662InformativeInherited
Fly Anatomy (FA)cell component0.01027InformativeInherited
Fly Anatomy (FA)wing disc0Highly InformativeDirect
Fly Anatomy (FA)female germline stem cell1.805e-06Highly 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)viscus0.6099Least InformativeInherited
Xenopus ANatomical entity (XAN)multi-tissue structure0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)embryonic structure0.003978Moderately InformativeInherited
Xenopus ANatomical entity (XAN)visual system0.2365Moderately InformativeInherited
Xenopus ANatomical entity (XAN)notochord0.0002128InformativeDirect
Xenopus ANatomical entity (XAN)endoderm0.0007442InformativeDirect
Xenopus ANatomical entity (XAN)anatomical direction0.001566InformativeInherited
Xenopus ANatomical entity (XAN)pharyngeal region0.003638InformativeInherited
Xenopus ANatomical entity (XAN)primordium0.01835InformativeInherited
Xenopus ANatomical entity (XAN)heart0.05807InformativeInherited
Xenopus ANatomical entity (XAN)eye primordium1.207e-05Highly 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 componentCytoplasm1.137e-07Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Post-translational modificationDevelopmental protein1.784e-05Moderately InformativeDirect
Post-translational modificationAcetylation1.74e-11Least InformativeDirect
Post-translational modificationPhosphoprotein1.228e-08Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond4.237e-11Moderately 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 ]