SUPERFAMILY 1.75 HMM library and genome assignments server

Aspartate/ornithine carbamoyltransferase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   ATC-like [ 53670] (2)
Superfamily:   Aspartate/ornithine carbamoyltransferase [ 53671]
Families:   Aspartate/ornithine carbamoyltransferase [ 53672] (3)


Superfamily statistics
Genomes (2,979) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 6,449 42,000 28
Proteins 6,430 41,963 28


Functional annotation
General category Metabolism
Detailed category Amino acids metabolism and transport

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) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0.00000000001383 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.057 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.03637 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.03039 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.00000000000001086 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.00003491 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.00000005737 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.000007043 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.0001232 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 0.01118 Moderately Informative Inherited
Biological Process (BP) pyrimidine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.3215 Informative Inherited
Biological Process (BP) nucleobase metabolic process 0.000000000001037 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound biosynthetic process 0.00000000000001086 Highly Informative Direct
Molecular Function (MF) transferase activity 0.0000000008188 Least Informative Direct
Molecular Function (MF) hydrolase activity 0.6793 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring one-carbon groups 0 Informative Direct
Molecular Function (MF) hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 0.000000000001387 Informative Direct
Molecular Function (MF) ligase activity 0.00006729 Informative Direct
Cellular Component (CC) cytoplasmic part 0.0004298 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.01108 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.02222 Least Informative Inherited
Cellular Component (CC) membrane 0.06202 Least Informative Inherited
Cellular Component (CC) organelle envelope 0.00008374 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 0.00000009384 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0.00133 Moderately Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring one-carbon groups0Least InformativeDirect
Enzyme Commission (EC)Ligases1Least InformativeInherited
Enzyme Commission (EC)Forming carbon-nitrogen bonds1Moderately InformativeInherited
Enzyme Commission (EC)Carbon--nitrogen ligases with glutamine as amido-N0.5347InformativeInherited
Enzyme Commission (EC)Carboxyl- and carbamoyltransferases0Highly InformativeDirect
Enzyme Commission (EC)Carbamoyl-phosphate synthase (glutamine-hydrolyzin0.0008941Highly InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring one-carbon groups0Moderately InformativeDirect
Enzyme Commission (EC)Ligases1Moderately InformativeInherited
Enzyme Commission (EC)Carbon--nitrogen ligases with glutamine as amido-N-donor0.7653InformativeInherited
Enzyme Commission (EC)Carboxyl- and carbamoyltransferases0Highly InformativeDirect
Enzyme Commission (EC)Carbamoyl-phosphate synthase (glutamine-hydrolyzing)0.0001529Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis0Moderately InformativeDirect
Biological processArginine biosynthesis0Highly InformativeDirect
Biological processArginine metabolism0Highly InformativeDirect
Biological processPyrimidine biosynthesis0Highly InformativeDirect
Biological processPolyamine biosynthesis0.000001547Highly InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)aromatic compound metabolism0Least InformativeDirect
UniPathway (UP)amino-acid metabolism0.00007391Least InformativeDirect
UniPathway (UP)amino-acid degradation4.527e-16Moderately InformativeDirect
UniPathway (UP)proteinogenic amino-acid biosynthesis0.0000000742Moderately InformativeDirect
UniPathway (UP)nitrogen metabolism1Moderately InformativeInherited
UniPathway (UP)amine and polyamine metabolism1Moderately InformativeInherited
UniPathway (UP)L-arginine biosynthesis0InformativeDirect
UniPathway (UP)UMP biosynthesis via de novo pathway0InformativeDirect
UniPathway (UP)L-arginine degradation0.00000000001187InformativeDirect
UniPathway (UP)putrescine metabolism0.00009155InformativeDirect
UniPathway (UP)amine and polyamine biosynthesis0.1805InformativeInherited
UniPathway (UP)L-arginine degradation via ADI pathway0Highly InformativeDirect
UniPathway (UP)putrescine biosynthesis via agmatine pathway0.0000000000003305Highly InformativeDirect
UniPathway (UP)urea cycle0.0000000313Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR006130 SSF53671 Protein matches
Abstract

This family contains two related enzymes:

  1. Aspartate carbamoyltransferase (ATCase) catalyzes the conversion of aspartate and carbamoyl phosphate to carbamoylaspartate, the second step in the de novo biosynthesis of pyrimidine nucleotides [PubMed3015959]. In prokaryotes ATCase consists of two subunits: a catalytic chain (gene pyrB) and a regulatory chain (gene pyrI), while in eukaryotes it is a domain in a multi- functional enzyme (called URA2 in yeast, rudimentary in Drosophila, and CAD in mammals [PubMed8098212]) that also catalyzes other steps of the biosynthesis of pyrimidines.
  2. Ornithine carbamoyltransferase (OTCase) catalyzes the conversion of ornithine and carbamoyl phosphate to citrulline. In mammals this enzyme participates in the urea cycle [PubMed2662961] and is located in the mitochondrial matrix. In prokaryotes and eukaryotic microorganisms it is involved in the biosynthesis of arginine. In some bacterial species it is also involved in the degradation of arginine [PubMed3109911] (the arginine deaminase pathway).
It has been shown [PubMed6379651] that these two enzymes are evolutionary related. The predicted secondary structure of both enzymes are similar and there are some regions of sequence similarities. One of these regions includes three residues which have been shown, by crystallographic studies [PubMed6377306], to be implicated in binding the phosphoryl group of carbamoyl phosphate.


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) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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 20 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 Aspartate/ornithine carbamoyltransferase 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 20 hidden Markov models representing the Aspartate/ornithine carbamoyltransferase 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) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]