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Carboxypeptidase regulatory domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Prealbumin-like [ 49451] (7)
Superfamily:   Carboxypeptidase regulatory domain-like [ 49464] (2)
Families:   Carboxypeptidase regulatory domain [ 49465] (2)
  Pre-dockerin domain [ 141082]


Superfamily statistics
Genomes (1,103) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 9,546 45,787 3
Proteins 8,812 44,560 3


Functional annotation
General category Regulation
Detailed category Other regulatory function

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) regulation of cellular process 0.6384 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.1458 Least Informative Inherited
Biological Process (BP) developmental process 0.006116 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.6689 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.01843 Least Informative Inherited
Biological Process (BP) response to stimulus 0.7797 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.003103 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.00009327 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.009731 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.002431 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.003923 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.0234 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.004776 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.007557 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.01139 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.08572 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.2457 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.1602 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.2414 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.198 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.6334 Moderately Informative Inherited
Biological Process (BP) proteolysis 0.0004542 Informative Direct
Biological Process (BP) biological adhesion 0.00000007894 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.0005833 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.0004785 Informative Direct
Biological Process (BP) generation of neurons 0.00000119 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.0000002328 Informative Direct
Biological Process (BP) regulation of cell development 0.000333 Informative Direct
Biological Process (BP) cell projection organization 0.002356 Informative Inherited
Biological Process (BP) cellular component movement 0.006504 Informative Inherited
Biological Process (BP) locomotion 0.00594 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.1631 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.02069 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.01845 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.01507 Informative Inherited
Biological Process (BP) chemotaxis 0.0001923 Highly Informative Direct
Biological Process (BP) cell adhesion 0.0000000577 Highly Informative Direct
Biological Process (BP) neuron projection development 0.0004343 Highly Informative Direct
Biological Process (BP) cell part morphogenesis 0.3798 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.03298 Highly Informative Inherited
Biological Process (BP) negative regulation of transcription, DNA-dependent 0.01495 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.0000000000002587 Least Informative Direct
Molecular Function (MF) binding 0.4559 Least Informative Inherited
Molecular Function (MF) peptidase activity 0.00000000001662 Informative Direct
Molecular Function (MF) protein dimerization activity 0.0000000005732 Informative Direct
Molecular Function (MF) exopeptidase activity 0 Highly Informative Direct
Molecular Function (MF) protein homodimerization activity 0.000000000006488 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.0001501 Highly Informative Direct
Cellular Component (CC) membrane 0.000004083 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.6361 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.7308 Least Informative Inherited
Cellular Component (CC) plasma membrane 0.0008082 Moderately Informative Direct
Cellular Component (CC) vesicle 0.00009464 Moderately Informative Direct
Cellular Component (CC) cell projection 0.00008997 Moderately Informative Direct
Cellular Component (CC) extracellular region part 0.000000001448 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.297 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.2442 Moderately Informative Inherited
Cellular Component (CC) intrinsic to membrane 0.005937 Moderately Informative Inherited
Cellular Component (CC) Golgi apparatus 0.00003476 Informative Direct
Cellular Component (CC) integral to membrane 0.000003739 Informative Direct
Cellular Component (CC) extracellular matrix 0.00005072 Informative Direct
Cellular Component (CC) synapse part 0.000006139 Informative Direct
Cellular Component (CC) extracellular membrane-bounded organelle 0.00001274 Informative Direct
Cellular Component (CC) nucleoplasm part 0.002406 Informative Inherited
Cellular Component (CC) nuclear body 0.0000007533 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)Metallocarboxypeptidases0Highly InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)pericellular component development variant0Moderately InformativeDirect
Worm Phenotype (WP)basement membrane remodeling variant0InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)viable0Least InformativeDirect
Fly Phenotype (FP)fertile0Moderately InformativeDirect

Document: FP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus DEvelopment stage (XDE)embryonic stage0Least InformativeDirect
Xenopus DEvelopment stage (XDE)NF stage0Least InformativeDirect

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Moderately InformativeDirect
Enzyme Commission (EC)Metallocarboxypeptidases0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDifferentiation0.0000006946Moderately InformativeDirect
Biological processCell adhesion0.00000000004392InformativeDirect
Cellular componentMembrane0.00000002647Least InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentCell projection0.000000000001082Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0.00000002882Moderately InformativeDirect
Cellular componentCell junction0.00002029Moderately InformativeDirect
Cellular componentSynapse0.0000001791InformativeDirect
Cellular componentExtracellular matrix0.0006662InformativeDirect
Cellular componentSynaptosome0.000000000004952Highly InformativeDirect
Cellular componentPostsynaptic cell membrane0.000000004054Highly InformativeDirect
DomainSignal9.229e-16Least InformativeDirect
DomainEGF-like domain0.00000000000009095InformativeDirect
Molecular functionZinc0.0000000000003555Least InformativeDirect
Post-translational modificationHydrolase0.00000000741Least InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationRepressor0.0000007777Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.0004351Moderately InformativeDirect
Post-translational modificationMetalloprotease0InformativeDirect
Post-translational modificationCarboxypeptidase0Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues0.0000000001136Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008969 SSF49464 Protein matches
Abstract

This domain identifies a number of eukaryotic carboxypeptidases, these include carboxypeptidase D, E (H), N, X, X2 and Z. These are metallopeptidases belong to MEROPS peptidase family M14 (clan MC), subfamily M14B.

Carboxypeptidase D (CPD) is a new B-type metallocarboxypeptidase that is membrane bound and has an acidic pH optimum. A hydrophobic region at the N-terminus represents the signal peptide, and one near the C-terminus that probably represents the transmembrane anchor. A regulatory domain within the protein has been identified as a beta-sandwich, comprising 7 strands in 2 sheets in a greek-key topology. Some family members have an additional 1-2 strands to the common fold [PubMed11080148].

The bacterial and archaeal sequences having this signature are variously annotated, examples are:

  • Hypothetical/conserved/membrane/cell surface protein
  • N-acetylglucosamine deacetylase
  • Side tail fibre protein homolog from lambdoid prophage Rac
  • Hypothetical tonB-linked outer membrane receptor
  • OmpA-related protein
  • Putative outer membrane protein, probably involved in nutrient binding
  • TonB-dependent receptor


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) · Enzyme Commission (EC) · Worm Phenotype (WP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · 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 3 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 Carboxypeptidase regulatory domain-like 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 3 hidden Markov models representing the Carboxypeptidase regulatory domain-like 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) · Enzyme Commission (EC) · Worm Phenotype (WP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]