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Composite domain of metallo-dependent hydrolases superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Composite domain of metallo-dependent hydrolases [ 51337]
Superfamily:   Composite domain of metallo-dependent hydrolases [ 51338] (11)
Families:   Cytosine deaminase [ 69373]
  alpha-Subunit of urease [ 51339]
  Hydantoinase (dihydropyrimidinase) [ 75044] (5)
  SAH/MTA deaminase-like [ 82224] (3)
  Isoaspartyl dipeptidase [ 89438]
  N-acetylglucosamine-6-phosphate deacetylase, NagA [ 82227]
  D-aminoacylase [ 82230]
  Adenine deaminase [ 141689]
  Zn-dependent arginine carboxypeptidase-like [ 159340] (3)
  Imidazolonepropionase-like [ 159347] (3)
  DR0824-like [ 159355]


Superfamily statistics
Genomes (2,938) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 23,997 218,554 88
Proteins 20,954 194,469 58


Functional annotation
General category Metabolism
Detailed category Other enzymes

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)In linear amides1Moderately InformativeInherited
Enzyme Commission (EC)In cyclic amides0InformativeDirect
Enzyme Commission (EC)In cyclic amidines1InformativeInherited
Enzyme Commission (EC)Urease0Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)syndrome0Moderately InformativeDirect

Document: DO 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)abnormal brain morphology0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal neuron morphology0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal cerebral hemisphere morphology0.00006213InformativeDirect
Mammalian Phenotype (MP)abnormal limbic system morphology0.08632InformativeInherited
Mammalian Phenotype (MP)abnormal hippocampus pyramidal cell layer0.000002849Highly InformativeDirect
Mammalian Phenotype (MP)abnormal hippocampus neuron morphology0.002218Highly InformativeInherited
Mammalian Phenotype (MP)abnormal neurite morphology0.01552Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)general pace of development variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Least InformativeDirect
Worm Phenotype (WP)retarded heterochronic variations0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect

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

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)nervous system0Least InformativeDirect
Zebrafish Anatomy (ZA)compound organ0Least InformativeDirect
Zebrafish Anatomy (ZA)organism subdivision0Least InformativeDirect
Zebrafish Anatomy (ZA)cell0Least InformativeDirect
Zebrafish Anatomy (ZA)central nervous system0Moderately InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)cavitated compound organ0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect

Document: AP 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 carbon-nitrogen bonds, other than peptide bonds0Moderately InformativeDirect
Enzyme Commission (EC)Ligases1Moderately InformativeInherited
Enzyme Commission (EC)Carbon--nitrogen ligases with glutamine as amido-N-donor0.8337InformativeInherited
Enzyme Commission (EC)In linear amides1InformativeInherited
Enzyme Commission (EC)In cyclic amidines1InformativeInherited
Enzyme Commission (EC)In cyclic amides0Highly InformativeDirect
Enzyme Commission (EC)Carbamoyl-phosphate synthase (glutamine-hydrolyzing)0.0004173Highly InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR011059 SSF51338 Protein matches
Abstract

The composite domain of metal-dependent hydrolases has a pseudo-barrel fold that is interrupted by the catalytic beta/alpha barrel domain. This domain is found in a variety of bacterial and fungal enzymes, including: cytosine deaminase, an enzyme that is important in the pyrimidine salvage pathway [PubMed11812140]; the alpha-subunit of urease, a virulence factor of gastric pathogens such as Helicobacter pylori [PubMed12127484]; D- and L-hydantoinases (dihydropyrimidinase), which catalyse the production of D- and L-amino acids, respectively [PubMed12837777]; isoaspartyl dipeptidase from Escherichia coli, which functions in protein degradation [PubMed12718528]; N-acetylglucosamine-6-phosphate deacetylase, which is an enzyme from the biosynthetic pathway to amino-sugar-nucleotides [PubMed14557261]; and N-acyl-D-amino acid amidohydrolase (D-aminoacylase), involved in the synthesis of D-amino acids [PubMed12454005].


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) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 33 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 Composite domain of metallo-dependent hydrolases 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 33 hidden Markov models representing the Composite domain of metallo-dependent hydrolases 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) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]