SUPERFAMILY 1.75 HMM library and genome assignments server


Carbamoyl phosphate synthetase, large subunit connection domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Carbamoyl phosphate synthetase, large subunit connection domain [ 48107]
Superfamily:   Carbamoyl phosphate synthetase, large subunit connection domain [ 48108]
Families:   Carbamoyl phosphate synthetase, large subunit connection domain [ 48109]


Superfamily statistics
Genomes (2,829) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,490 23,193 3
Proteins 3,483 23,171 3


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) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 3.91e-11 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.01324 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.007631 Least Informative Inherited
Biological Process (BP) response to stimulus 0.5165 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.006138 Least Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 1.938e-15 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 1.855e-12 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 3.755e-11 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 4.3e-07 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 2.288e-06 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 9.43e-06 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.0001229 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.001673 Moderately Informative Inherited
Biological Process (BP) pyrimidine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) response to lipid 0.0008835 Informative Direct
Biological Process (BP) amide biosynthetic process 0.008989 Informative Inherited
Biological Process (BP) pyrimidine-containing compound biosynthetic process 0 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 0 Highly Informative Direct
Molecular Function (MF) binding 0.4655 Least Informative Inherited
Molecular Function (MF) hydrolase activity 0.2842 Least Informative Inherited
Molecular Function (MF) transferase activity 0.1873 Least Informative Inherited
Molecular Function (MF) cation binding 0.01686 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.2163 Moderately Informative Inherited
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 8.977e-15 Informative Direct
Molecular Function (MF) hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 1.797e-10 Informative Direct
Molecular Function (MF) carboxylic acid binding 2.398e-09 Informative Direct
Molecular Function (MF) amino acid binding 9.468e-11 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)Ligases0Least InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups1Least InformativeInherited
Enzyme Commission (EC)Forming carbon-nitrogen bonds0Moderately InformativeDirect
Enzyme Commission (EC)Carbon--nitrogen ligases with glutamine as amido-N0InformativeDirect
Enzyme Commission (EC)In cyclic amides0.00091InformativeDirect
Enzyme Commission (EC)Carbamoyl-phosphate synthase (glutamine-hydrolyzin0Highly InformativeDirect
Enzyme Commission (EC)Dihydroorotase8.05e-06Highly InformativeDirect
Enzyme Commission (EC)Carboxyl- and carbamoyltransferases1.407e-05Highly InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds0.9828Moderately InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups1Moderately InformativeInherited
Enzyme Commission (EC)Carbon--nitrogen ligases with glutamine as amido-N-donor0InformativeDirect
Enzyme Commission (EC)Other carbon--nitrogen ligases1InformativeInherited
Enzyme Commission (EC)Carbamoyl-phosphate synthase (glutamine-hydrolyzing)0Highly InformativeDirect
Enzyme Commission (EC)Carbamoyl-phosphate synthase (ammonia)8.001e-14Highly InformativeDirect
Enzyme Commission (EC)Carboxyl- and carbamoyltransferases1.369e-06Highly InformativeDirect
Enzyme Commission (EC)In cyclic amides0.0001125Highly 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 processPyrimidine biosynthesis0Highly InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Post-translational modificationLigase0Moderately 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 metabolism0Least InformativeDirect
UniPathway (UP)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)UMP biosynthesis via de novo pathway0InformativeDirect
UniPathway (UP)L-arginine biosynthesis0InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR005480 SSF48108 Protein matches
Abstract

Carbamoyl-phosphate synthase (CPSase) catalyzes the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate [PubMed1972379]. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and pyrimidines. Glutamine-dependent CPSase (CPSase II) is involved in the biosynthesis of pyrimidines and purines.

In bacteria such as Escherichia coli, a single enzyme is involved in both biosynthetic pathways while other bacteria have separate enzymes. The bacterial enzymes are formed of two subunits. A small chain (carA) that provides glutamine amidotransferase activity (GATase) necessary for removal of the ammonia group from glutamine, and a large chain (carB) that provides CPSase activity. The large subunit consists of four structural units: the carboxyphosphate synthetic component, the oligomerization domain, the carbamoyl phosphate synthetic component and the allosteric domain [PubMed10089390]. Such a structure is also present in fungi for arginine biosynthesis (CPA1 and CPA2).

Two main CPSases have been identified in mammals, CPSase I is mitochondrial, is found in high levels in the liver and is involved in arginine biosynthesis; while CPSase II is cytosolic, is associated with aspartate carbamoyltransferase (ATCase) and dihydroorotase (DHOase) and is involved in pyrimidine biosynthesis. In the pyrimidine pathway in most eukaryotes, CPSase is found as a domain in a multi-functional protein, which also has GATase, ACTase and DHOase activity. Ammonia-dependent CPSase (CPSase I) is involved in the urea cycle in ureolytic vertebrates and is a monofunctional protein located in the mitochondrial matrix. The CPSase domain is typically 120 kD in size and has arisen from the duplication of an ancestral subdomain of about 500 amino acids. Each subdomain independently binds to ATP and it is suggested that the two homologous halves act separately, one to catalyze the phosphorylation of bicarbonate to carboxyphosphate and the other that of carbamate to carbamyl phosphate. The CPSase subdomain is also present in a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (ACC), propionyl-CoA carboxylase (PCCase), pyruvate carboxylase (PC) and urea carboxylase .


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 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 Carbamoyl phosphate synthetase, large subunit connection 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 Carbamoyl phosphate synthetase, large subunit connection 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) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]