2YWC

Crystal structure of GMP synthetase from Thermus thermophilus in complex with XMP

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d2ywcd1	Alpha and beta proteins (a/b)	Flavodoxin-like	Class I glutamine amidotransferase-like	Class I glutamine amidotransferases (GAT)	GMP synthetase	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
D	d2ywcd2	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	N-type ATP pyrophosphatases	GMP synthetase, central domain	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
D	d2ywcd3	Alpha and beta proteins (a+b)	Alpha-lytic protease prodomain-like	GMP synthetase C-terminal dimerisation domain	GMP synthetase C-terminal dimerisation domain	GMP synthetase C-terminal dimerisation domain	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
A	d2ywca1	Alpha and beta proteins (a/b)	Flavodoxin-like	Class I glutamine amidotransferase-like	Class I glutamine amidotransferases (GAT)	GMP synthetase	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
A	d2ywca2	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	N-type ATP pyrophosphatases	GMP synthetase, central domain	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
A	d2ywca3	Alpha and beta proteins (a+b)	Alpha-lytic protease prodomain-like	GMP synthetase C-terminal dimerisation domain	GMP synthetase C-terminal dimerisation domain	GMP synthetase C-terminal dimerisation domain	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
B	d2ywcb1	Alpha and beta proteins (a/b)	Flavodoxin-like	Class I glutamine amidotransferase-like	Class I glutamine amidotransferases (GAT)	GMP synthetase	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
B	d2ywcb2	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	N-type ATP pyrophosphatases	GMP synthetase, central domain	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
B	d2ywcb3	Alpha and beta proteins (a+b)	Alpha-lytic protease prodomain-like	GMP synthetase C-terminal dimerisation domain	GMP synthetase C-terminal dimerisation domain	GMP synthetase C-terminal dimerisation domain	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
C	d2ywcc1	Alpha and beta proteins (a/b)	Flavodoxin-like	Class I glutamine amidotransferase-like	Class I glutamine amidotransferases (GAT)	GMP synthetase	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
C	d2ywcc2	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	N-type ATP pyrophosphatases	GMP synthetase, central domain	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
C	d2ywcc3	Alpha and beta proteins (a+b)	Alpha-lytic protease prodomain-like	GMP synthetase C-terminal dimerisation domain	GMP synthetase C-terminal dimerisation domain	GMP synthetase C-terminal dimerisation domain	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	GMP_synt_C	e2ywcD3	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: GMP synthetase C-terminal dimerisation domain (From Topology)	T: GMP synthetase C-terminal dimerisation domain	F: GMP_synt_C	ECOD (1.6)
D	NAD_synthase	e2ywcD1	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: NAD_synthase	ECOD (1.6)
D	GATase	e2ywcD2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: GATase	ECOD (1.6)
A	GMP_synt_C	e2ywcA3	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: GMP synthetase C-terminal dimerisation domain (From Topology)	T: GMP synthetase C-terminal dimerisation domain	F: GMP_synt_C	ECOD (1.6)
A	NAD_synthase	e2ywcA1	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: NAD_synthase	ECOD (1.6)
A	GATase	e2ywcA2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: GATase	ECOD (1.6)
B	GMP_synt_C	e2ywcB3	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: GMP synthetase C-terminal dimerisation domain (From Topology)	T: GMP synthetase C-terminal dimerisation domain	F: GMP_synt_C	ECOD (1.6)
B	NAD_synthase	e2ywcB1	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: NAD_synthase	ECOD (1.6)
B	GATase	e2ywcB2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: GATase	ECOD (1.6)
C	GMP_synt_C	e2ywcC3	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: GMP synthetase C-terminal dimerisation domain (From Topology)	T: GMP synthetase C-terminal dimerisation domain	F: GMP_synt_C	ECOD (1.6)
C	NAD_synthase	e2ywcC1	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: NAD_synthase	ECOD (1.6)
C	GATase	e2ywcC2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: GATase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)
D	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
D	3.30.300.10	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)
A	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)
A	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
A	3.30.300.10	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)
B	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)
B	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
B	3.30.300.10	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)
C	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)
C	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
C	3.30.300.10	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00117	Glutamine amidotransferase class-I (GATase)	Glutamine amidotransferase class-I	-	Domain
A, B, C, D	PF00958	GMP synthase C terminal domain (GMP_synt_C)	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 Swiss:P49915 EC:6.3.5.2. In prokaryotes this domain mediates dimerisation. Eukaryotic GMP ...	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 Swiss: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.	Domain
A, B, C, D	PF07722	Peptidase C26 (Peptidase_C26)	Peptidase C26	These peptidases have gamma-glutamyl hydrolase activity; that is they catalyse the cleavage of the gamma-glutamyl bond in poly-gamma-glutamyl substrates. They are structurally related to Pfam:PF00117, but contain extensions in four loops and at the C ...	These peptidases have gamma-glutamyl hydrolase activity; that is they catalyse the cleavage of the gamma-glutamyl bond in poly-gamma-glutamyl substrates. They are structurally related to Pfam:PF00117, but contain extensions in four loops and at the C terminus [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	GMP synthase [glutamine-hydrolyzing]	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding carbon-nitrogen ligase activity, with glutamine as amido-N-donor GMP synthase activity GMP synthase (glutamine-hydrolyzing) activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity	glutamine metabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process glutamine family amino acid metabolic process proteinogenic amino acid metabolic process metabolic process cellular process small molecule metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR029062	Class I glutamine amidotransferase-like	Homologous Superfamily
A, B, C, D	IPR022955	GMP synthase	Family
A, B, C, D	IPR001674	GMP synthase, C-terminal	Domain
A, B, C, D	IPR017926	Glutamine amidotransferase	Domain
A, B, C, D	IPR004739	GMP synthase, glutamine amidotransferase	Domain
A, B, C, D	IPR025777	GMP synthetase ATP pyrophosphatase domain	Domain
A, B, C, D	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.