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33  structures 8397  species 5  interactions 9042  sequences 58  architectures

Family: GMP_synt_C (PF00958)

Summary: GMP synthase C terminal domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "GMP synthase". More...

GMP synthase Edit Wikipedia article

GMP synthetase
(glutamine-hydrolyzing)
2vxo.jpg
GMP synthetase, human
Identifiers
EC number6.3.5.2
CAS number37318-71-1
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structuresRCSB PDB PDBe PDBsum
Gene OntologyAmiGO / QuickGO
GMP synthetase C terminal domain
PDB 1gpm EBI.jpg
escherichia coli gmp synthetase complexed with amp and pyrophosphate.[1]
Identifiers
SymbolGMP_synt_C
PfamPF00958
InterProIPR001674
PROSITEPDOC00405
SCOPe1gpm / SUPFAM
GMPS
Protein GMPS PDB 2VPI.png
Available structures
PDBOrtholog search: PDBe RCSB
Identifiers
AliasesGMPS, GMP synthase, guanine monophosphate synthase, GATD7, GMP synthase
External IDsOMIM: 600358 MGI: 2448526 HomoloGene: 68367 GeneCards: GMPS
Gene location (Human)
Chromosome 3 (human)
Chr.Chromosome 3 (human)[2]
Chromosome 3 (human)
Genomic location for GMPS
Genomic location for GMPS
Band3q25.31Start155,870,650 bp[2]
End155,944,020 bp[2]
RNA expression pattern
PBB GE GMPS 214431 at fs.png
More reference expression data
Orthologs
SpeciesHumanMouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_003875

NM_001033300

RefSeq (protein)

NP_003866

NP_001028472

Location (UCSC)Chr 3: 155.87 – 155.94 MbChr 3: 63.98 – 64.02 Mb
PubMed search[4][5]
Wikidata
View/Edit HumanView/Edit Mouse

Guanosine monophosphate synthetase, (EC 6.3.5.2) also known as GMPS is an enzyme that converts xanthosine monophosphate to guanosine monophosphate.[6]

In the de novo synthesis of purine nucleotides, IMP is the branch point metabolite at which point the pathway diverges to the synthesis of either guanine or adenine nucleotides. In the guanine nucleotide pathway, there are 2 enzymes involved in converting IMP to GMP, namely IMP dehydrogenase (IMPD1), which catalyzes the oxidation of IMP to XMP, and GMP synthetase, which catalyzes the amination of XMP to GMP.[6]

Enzymology

In enzymology, a GMP synthetase (glutamine-hydrolysing) (EC 6.3.5.2) is an enzyme that catalyzes the chemical reaction

ATP + xanthosine 5'-phosphate + L-glutamine + H2O AMP + diphosphate + GMP + L-glutamate

The 4 substrates of this enzyme are ATP, xanthosine 5'-phosphate, L-glutamine, and H2O, whereas its 4 products are AMP, diphosphate, GMP, and L-glutamate.

This enzyme belongs to the family of ligases, specifically those forming carbon-nitrogen bonds carbon-nitrogen ligases with glutamine as amido-N-donor. The systematic name of this enzyme class is xanthosine-5'-phosphate:L-glutamine amido-ligase (AMP-forming). Other names in common use include GMP synthetase (glutamine-hydrolysing), guanylate synthetase (glutamine-hydrolyzing), guanosine monophosphate synthetase (glutamine-hydrolyzing), xanthosine 5'-phosphate amidotransferase, and guanosine 5'-monophosphate synthetase. This enzyme participates in purine metabolism and glutamate metabolism. At least one compound, Psicofuranin is known to inhibit this enzyme.

Structural studies

As of late 2007, 5 structures have been solved for this class of enzymes, with PDB accession codes 1GPM, 1WL8, 2A9V, 2D7J, and 2DPL.

References

  1. ^ Tesmer JJ, Klem TJ, Deras ML, Davisson VJ, Smith JL (January 1996). "The crystal structure of GMP synthetase reveals a novel catalytic triad and is a structural paradigm for two enzyme families". Nat. Struct. Biol. 3 (1): 74–86. doi:10.1038/nsb0196-74. PMID 8548458.
  2. ^ a b c GRCh38: Ensembl release 89: ENSG00000163655 - Ensembl, May 2017
  3. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000027823 - Ensembl, May 2017
  4. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  6. ^ a b "Entrez Gene: GMPS guanine monphosphate synthetase".

Further reading

External links


This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

GMP synthase C terminal domain Provide feedback

GMP synthetase is a glutamine amidotransferase from the de novo purine biosynthetic pathway. This family is the C-terminal domain specific to the GMP synthases P49915 EC:6.3.5.2. In prokaryotes this domain mediates dimerisation. Eukaryotic GMP synthases are monomers. This domain in eukaryotes includes several large insertions that may form globular domains.

Literature references

  1. Tesmer JJ, Klem TJ, Deras ML, Davisson VJ, Smith JL; , Nat Struct Biol 1996;3:74-86.: The crystal structure of GMP synthetase reveals a novel catalytic triad and is a structural paradigm for two enzyme families. PUBMED:8548458 EPMC:8548458


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001674

The amidotransferase family of enzymes utilises the ammonia derived from the hydrolysis of glutamine for a subsequent chemical reaction catalyzed by the same enzyme. The ammonia intermediate does not dissociate into solution during the chemical transformations [PUBMED:10387030]. GMP synthetase is a glutamine amidotransferase from the de novo purine biosynthetic pathway. The C-terminal domain is specific to the GMP synthases EC. In prokaryotes this domain mediates dimerisation. Eukaryotic GMP synthases are monomers. This domain in eukaryotes includes several large insertions that may form globular domains [PUBMED:8548458].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(235)
Full
(9042)
Representative proteomes UniProt
(24692)
NCBI
(29711)
Meta
(2109)
RP15
(2406)
RP35
(6044)
RP55
(8972)
RP75
(12473)
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PP/heatmap 1                

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(235)
Full
(9042)
Representative proteomes UniProt
(24692)
NCBI
(29711)
Meta
(2109)
RP15
(2406)
RP35
(6044)
RP55
(8972)
RP75
(12473)
Alignment:
Format:
Order:
Sequence:
Gaps:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(235)
Full
(9042)
Representative proteomes UniProt
(24692)
NCBI
(29711)
Meta
(2109)
RP15
(2406)
RP35
(6044)
RP55
(8972)
RP75
(12473)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_1137 (release 3.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Bateman A , Griffiths-Jones SR
Number in seed: 235
Number in full: 9042
Average length of the domain: 91.20 aa
Average identity of full alignment: 52 %
Average coverage of the sequence by the domain: 18.13 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.1 21.1
Trusted cut-off 21.8 21.1
Noise cut-off 20.7 21.0
Model length: 92
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Interactions

There are 5 interactions for this family. More...

NAD_synthase NAD_synthase GMP_synt_C GATase GATase

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the GMP_synt_C domain has been found. There are 33 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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