SUPERFAMILY 1.75 HMM library and genome assignments server

Glutamine synthetase, N-terminal domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   beta-Grasp (ubiquitin-like) [ 54235] (14)
Superfamily:   Glutamine synthetase, N-terminal domain [ 54368]
Families:   Glutamine synthetase, N-terminal domain [ 54369]


Superfamily statistics
Genomes (2,726) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 5,585 27,553 4
Proteins 5,581 27,547 4


Functional annotation
General category Metabolism
Detailed category Coenzyme 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 0.00000002946 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.0008739 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.1056 Least Informative Inherited
Biological Process (BP) response to stimulus 0.07728 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.03522 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.000000000002984 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0.00001197 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.00006207 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.00009311 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.009392 Moderately Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.003238 Informative Inherited
Biological Process (BP) response to carbohydrate 0.000000003581 Highly Informative Direct
Molecular Function (MF) ligase activity 0 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)Lyases0.9467Least InformativeInherited
Enzyme Commission (EC)Forming carbon-nitrogen bonds0Moderately InformativeDirect
Enzyme Commission (EC)Carboxy-lyases0.0002424Moderately InformativeDirect
Enzyme Commission (EC)Acid--ammonia (or amide) ligases (amide synthases)0Highly InformativeDirect
Enzyme Commission (EC)Glutamate decarboxylase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0.9815Least InformativeInherited
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-carbon lyases0.005256Moderately InformativeInherited
Enzyme Commission (EC)Carboxy-lyases0.0002114InformativeDirect
Enzyme Commission (EC)Acid--ammonia (or amide) ligases (amide synthases)0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processNitrogen fixation0InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
DomainTransit peptide0.00001385Moderately InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationUbl conjugation0.0001161Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008147 SSF54368 Protein matches
Abstract

Glutamine synthetase (GS) [PubMed2900091] plays an essential role in the metabolism of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine.

There seem to be three different classes of GS [PubMed8096645, PubMed2575672, PubMed7916055]:

  • Class I enzymes (GSI) are specific to prokaryotes, and are oligomers of 12 identical subunits. The activity of GSI-type enzyme is controlled by the adenylation of a tyrosine residue. The adenylated enzyme is inactive (see ).
  • Class II enzymes (GSII) are found in eukaryotes and in bacteria belonging to the Rhizobiaceae, Frankiaceae, and Streptomycetaceae families (these bacteria have also a class-I GS). GSII are octamer of identical subunits. Plants have two or more isozymes of GSII, one of the isozymes is translocated into the chloroplast.
  • Class III enzymes (GSIII) has, currently, only been found in Bacteroides fragilis and in Butyrivibrio fibrisolvens. It is a hexamer of identical chains. It is much larger (about 700 amino acids) than the GSI (450 to 470 amino acids) or GSII (350 to 420 amino acids) enzymes.

While the three classes of GS's are clearly structurally related, the sequence similarities are not so extensive.


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) · Worm Phenotype (WP) · Arabidopsis Plant Ontology (AP) · 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 Glutamine synthetase, N-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 Glutamine synthetase, N-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) · Worm Phenotype (WP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]