2YWB | pdb_00002ywb

Crystal structure of GMP synthetase from Thermus thermophilus

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)
A	d2ywba1	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	d2ywba2	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	d2ywba3	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	d2ywbb1	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	d2ywbb2	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	d2ywbb3	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	d2ywbc1	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	d2ywbc2	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	d2ywbc3	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)
D	d2ywbd1	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	d2ywbd2	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	d2ywbd3	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)
A		e2ywbA1	A: HTH	X: HTH	H: winged helix domain	T: tRNA-synt_1b	F:	ECOD (20:10:01)
B		e2ywbB1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: Rpf1_C	F:	ECOD (20:10:01)
C		e2ywbC1	A: HTH	X: HTH	H: winged helix domain	T: tRNA-synt_1b	F:	ECOD (20:10:01)
D		e2ywbD1	A: HTH	X: HTH	H: winged helix domain	T: tRNA-synt_1b	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

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

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 anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide 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	-	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.