SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


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 (2,837) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 3,509 28,610 3
Proteins 3,502 28,554 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) cellular aromatic compound metabolic process 0.0002843 Least Informative Direct
Biological Process (BP) biosynthetic process 0.000000000004663 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.00000001425 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.000000000000001925 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0002311 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0006553 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) primary metabolic process 0.3017 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.5832 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.2255 Least Informative Inherited
Biological Process (BP) biological regulation 0.5008 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.00000000005214 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.00000005092 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.0000002958 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 0.05101 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.01827 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.04278 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.04031 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.01796 Moderately Informative Inherited
Biological Process (BP) animal organ development 0.002594 Moderately Informative Inherited
Biological Process (BP) amide biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) glutamine family amino acid metabolic process 0.00000003369 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.0007377 Informative Direct
Biological Process (BP) circulatory system development 0.0001309 Informative Direct
Biological Process (BP) pyrimidine-containing compound biosynthetic process 0 Informative Direct
Biological Process (BP) cell development 0.0311 Informative Inherited
Biological Process (BP) generation of neurons 0.003701 Informative Inherited
Biological Process (BP) central nervous system development 0.001585 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.001317 Informative Inherited
Biological Process (BP) nucleobase metabolic process 0 Highly Informative Direct
Biological Process (BP) camera-type eye development 0.0000006944 Highly Informative Direct
Biological Process (BP) neuron development 0.0003424 Highly Informative Direct
Biological Process (BP) regulation of cellular response to growth factor stimulus 0.0000001075 Highly Informative Direct
Biological Process (BP) plasma membrane bounded cell projection organization 0.0005097 Highly Informative Direct
Molecular Function (MF) binding 0.1928 Least Informative Inherited
Molecular Function (MF) hydrolase activity 0.5685 Least Informative Inherited
Molecular Function (MF) transferase activity 0.4368 Least Informative Inherited
Molecular Function (MF) small molecule binding 0.000865 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0.0001811 Moderately Informative Direct
Molecular Function (MF) anion binding 0.1978 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.0000000000004249 Informative Direct
Molecular Function (MF) hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 0.000000003403 Informative Direct
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) purine nucleotide binding 0.00001044 Informative Direct
Molecular Function (MF) carboxylic acid binding 0.000000007338 Informative Direct
Molecular Function (MF) ribonucleotide binding 0.00001194 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.000004677 Informative Direct
Molecular Function (MF) ATP binding 0.0000006087 Highly Informative Direct
Molecular Function (MF) amino acid binding 0.00000000001544 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)Dihydroorotase0.00000805Highly InformativeDirect
Enzyme Commission (EC)Carboxyl- and carbamoyltransferases0.00001407Highly 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 processPyrimidine biosynthesis0Highly InformativeDirect
Biological processArginine biosynthesis0Highly InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionManganese0Moderately InformativeDirect

Document: KW 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) · 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 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) · UniProtKB KeyWords (KW) · Internal database links ]