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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 (2,162) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 2,881 16,311 3
Proteins 2,854 16,253 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 0.0000000003374 Least Informative Direct
Biological Process (BP) biosynthetic process 0.0005374 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.0008489 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.00116 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.7935 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0.0000001146 Moderately Informative Direct
Biological Process (BP) glutamine family amino acid metabolic process 0 Informative Direct
Biological Process (BP) dicarboxylic acid metabolic process 0.0000000000001618 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.0000168 Informative Direct
Biological Process (BP) dicarboxylic acid biosynthetic process 0 Highly Informative Direct
Biological Process (BP) glutamate metabolic process 0.000000002896 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-NH2 group of donors 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.269 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.9589 Least Informative Inherited
Cellular Component (CC) plastid 0.000009488 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)0.00000007489Highly 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 processMethanogenesis0Highly InformativeDirect
Cellular componentPlastid0.0000000000002417Moderately InformativeDirect
DomainTransit peptide0.0003323Moderately InformativeDirect
DomainGlutamine amidotransferase0Highly InformativeDirect
Molecular functionMetal-binding0.0000001251Least InformativeDirect
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionIron-sulfur0Moderately InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionNADP0.0003608Moderately InformativeDirect
Molecular functionFMN0InformativeDirect
Molecular functionFAD0.0007333InformativeDirect
Molecular function3Fe-4S0Highly InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect

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