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24  structures 4651  species 3  interactions 4898  sequences 31  architectures

# 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

GMP synthase
Identifiers
EC number 6.3.4.1
CAS number 9023-55-6
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum

GMP synthase (EC 6.3.4.1, xanthosine-5'-phosphateâammonia ligase, guanylate synthetase, XMP aminase, xanthosine 5'-monophosphate aminase) is an enzyme with system name xanthosine-5'-phosphate:ammonia ligase (AMP-forming).[1] This enzyme catalyses the following chemical reaction

ATP + XMP + NH3 $\rightleftharpoons$ AMP + diphosphate + GMP

## References

1. ^ Moyed, H.S. and Magasanik, B. (1957). "Enzymes essential for the biosynthesis of nucleic acid guanine; xanthosine 5â²-phosphate aminase of Aerobacter aerogenes". J. Biol. Chem. 226: 351â363. PMID 13428768.

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

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

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...

# 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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

## View options

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
(161)
Full
(4898)
Representative proteomes NCBI
(3535)
Meta
(2105)
RP15
(423)
RP35
(820)
RP55
(1086)
RP75
(1280)
Jalview View  View  View  View  View  View  View  View
HTML View  View  View  View  View  View
PP/heatmap 1 View  View  View  View  View
Pfam viewer View  View

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

Key: available, not generated, not available.

## Format an alignment

Seed
(161)
Full
(4898)
Representative proteomes NCBI
(3535)
Meta
(2105)
RP15
(423)
RP35
(820)
RP55
(1086)
RP75
(1280)
Alignment:
Format:
Order:
Sequence:
Gaps:

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
(161)
Full
(4898)
Representative proteomes NCBI
(3535)
Meta
(2105)
RP15
(423)
RP35
(820)
RP55
(1086)
RP75
(1280)

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

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

 Pfam alignments: Seed (161) Full (4898)

# 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.

# 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

 Seed source: Pfam-B_1137 (release 3.0) Previous IDs: none Type: Domain Author: Finn RD, Bateman A, Griffiths-Jones SR Number in seed: 161 Number in full: 4898 Average length of the domain: 95.50 aa Average identity of full alignment: 57 % Average coverage of the sequence by the domain: 18.75 %

## HMM information

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.1 21.1
Trusted cut-off 21.1 21.4
Noise cut-off 20.9 20.7
Model length: 93
Family (HMM) version: 17

# Species distribution

### Sunburst controls

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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...

### Tree controls

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# Interactions

There are 3 interactions for this family. More...

# 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 24 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 seqence.