SUPERFAMILY 1.75 HMM library and genome assignments server

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Hedgehog/DD-peptidase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Hedgehog/DD-peptidase [ 55165]
Superfamily:   Hedgehog/DD-peptidase [ 55166] (5)
Families:   Muramoyl-pentapeptide carboxypeptidase [ 55167]
  MepA-like [ 111019]
  VanX-like [ 111022]
  Hedgehog (development protein), N-terminal signaling domain [ 55170] (2)
  VanY-like [ 160436]


Superfamily statistics
Genomes (1,838) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 4,406 40,374 7
Proteins 4,399 40,335 7


Functional annotation
General category Processes_EC
Detailed category Cell adhesion

Document:
Function annotation of SCOP domain superfamilies

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)Dipeptidases0.00000002089Highly InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of limbs0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the lower limb0Moderately InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0Least InformativeDirect
Mammalian Phenotype (MP)abnormal digestive system morphology0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal gland morphology0Moderately InformativeDirect

Document: MP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA 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)tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)trunk0Least InformativeDirect
Xenopus ANatomical entity (XAN)nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)cavitated compound organ0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)embryonic structure0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)brain0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)intestine0InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region0InformativeDirect
Xenopus ANatomical entity (XAN)neural plate0InformativeDirect
Xenopus ANatomical entity (XAN)eye0InformativeDirect
Xenopus ANatomical entity (XAN)epithelium0InformativeDirect
Xenopus ANatomical entity (XAN)marginal zone0Highly InformativeDirect
Xenopus ANatomical entity (XAN)hindbrain0Highly InformativeDirect
Xenopus DEvelopment stage (XDE)embryonic stage0Moderately InformativeDirect
Xenopus DEvelopment stage (XDE)NF stage 100Highly 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 (peptidases)0Moderately InformativeDirect
Enzyme Commission (EC)Dipeptidases0.0000000007567Highly InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR009045 SSF55166 Protein matches
Abstract

Hedgehog is a family of secreted signal molecules required for embryonic cell differentiation. Members of this family are composed of two domains. These proteins are autocatalytically cleaved by the C-terminal domain . This entry represents the zinc-binding domain found in the N-terminal region of Hedgehog proteins, and is responsible for both local and long-range signalling activities.

The structure of this domain is known [PubMed7477329] and reveals a tetrahedrally coordinated zinc ion that is structurally homologous to the zinc-binding motif in bacterial D-alanyl-D-alanine carboxypeptidases (DD-peptidases), but it is not necessarily found at the N-terminus in these proteins. The DD-peptidase family contains many penicillin binding proteins that remove the terminal D-alanine from peptide side chains of peptidoglycan [PubMed9841666].


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 · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) ]

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 9 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 Hedgehog/DD-peptidase 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 9 hidden Markov models representing the Hedgehog/DD-peptidase 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 · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · Internal database links ]