SUPERFAMILY 1.75 HMM library and genome assignments server


Alpha subunit of glutamate synthase, C-terminal domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Single-stranded right-handed beta-helix [ 51125] (8)
Superfamily:   Alpha subunit of glutamate synthase, C-terminal domain [ 69336]
Families:   Alpha subunit of glutamate synthase, C-terminal domain [ 69337]


Superfamily statistics
Genomes (2,156) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 2,870 14,172 3
Proteins 2,843 14,144 3


Functional annotation
General category Metabolism
Detailed category Other enzymes

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) single-organism metabolic process 1.424e-05 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.00795 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.008416 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 2.217e-09 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 7.494e-05 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.001625 Moderately Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.02963 Informative Inherited
Biological Process (BP) glutamate metabolic process 0.0008031 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity 1.341e-09 Moderately Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors0.0007678Moderately InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.0003024InformativeDirect
Enzyme Commission (EC)With an iron-sulfur protein as acceptor0Highly InformativeDirect
Enzyme Commission (EC)With other acceptors0Highly InformativeDirect
Enzyme Commission (EC)Glutamate synthase (NADH)7.489e-08Highly InformativeDirect

Document: EC annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

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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)megasporophyll0Least 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)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)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Acting on the CH-NH(2) group of donors0InformativeDirect
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors0.001202InformativeInherited
Enzyme Commission (EC)With other acceptors0Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.00015Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis1.398e-15Moderately InformativeDirect
Biological processMethanogenesis0Highly InformativeDirect
Cellular componentPlastid1.299e-13Moderately InformativeDirect
DomainTransit peptide0.0002951Moderately InformativeDirect
DomainGlutamine amidotransferase0Highly InformativeDirect
Molecular functionMetal-binding1.408e-07Least InformativeDirect
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionNAD0.0002703Moderately InformativeDirect
Molecular functionFMN0InformativeDirect
Molecular functionIron-sulfur0InformativeDirect
Molecular functionNADP0.0004693InformativeDirect
Molecular functionFAD0.0006779InformativeDirect
Molecular function3Fe-4S0Highly InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism1.011e-07Least InformativeDirect
UniPathway (UP)nitrogen metabolism0Moderately InformativeDirect
UniPathway (UP)organic acid metabolism0Moderately InformativeDirect
UniPathway (UP)one-carbon metabolism2.837e-14Moderately InformativeDirect
UniPathway (UP)proteinogenic amino-acid biosynthesis3.136e-09Moderately InformativeDirect
UniPathway (UP)L-glutamate metabolism0InformativeDirect
UniPathway (UP)organic acid biosynthesis0InformativeDirect
UniPathway (UP)methanogenesis1.711e-09InformativeDirect
UniPathway (UP)L-glutamate biosynthesis0Highly InformativeDirect
UniPathway (UP)methanogenesis from CO(2)0Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR002489 SSF69336 Protein matches
Abstract

Glutamate synthase (GltS) is a complex iron-sulphur flavoprotein that catalyses the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the bacterial, yeast and plant pathways for ammonia assimilation [PubMed11188694]. GltS is a multifunctional enzyme that functions through three distinct active centres carrying out multiple reaction steps: L-glutamine hydrolysis, conversion of 2-oxoglutarate into L-glutamate, and electron uptake from an electron donor. The active centres are synchronised to avoid the wasteful consumption of L-glutamine [PubMed11967268].. There are three classes of GltS, which share many functional properties: bacterial NADPH-dependent GltS, ferredoxin-dependent GltS from photosynthetic cells, and NAD(P)H-dependent GltS from yeast, fungi and lower animals.

The dimeric alpha subunits each consist of four domains: N-terminal amidotransferase domain, the central domain, the FMN binding domain and the C-terminal domain. The C-terminal domain forms a right-handed beta-helix that comprises seven helical turns [PubMed11188694]. Each helical turn has a sharp bend that is associated with a repeated sequence motif consisting of G-XX-G-XXX-G. This domain does not contain any residues directly involved in catalysis, but has a crucial structural role.

This domain is also found in proteins such as subunit C of formylmethanofuran dehydrogenase, which catalyses the first step in methane formation from carbon dioxide in methanogenic archaea. There are two isoenzymes of formylmethanofuran dehydrogenase: a tungsten-containing isoenzyme (FwdC) and a molybdenum-containing isoenzyme (FmdC). The tungsten isoenzyme is constitutively transcribed, whereas transcription of the molybdenum operon is induced by molybdate [PubMed9818358].


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) · Arabidopsis Plant Ontology (AP) · 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 2 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 Alpha subunit of glutamate synthase, C-terminal 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 2 hidden Markov models representing the Alpha subunit of glutamate synthase, C-terminal 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) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]