2YYE | pdb_00002yye

Crystal structure of selenophosphate synthetase from Aquifex aeolicus complexed with AMPCPP

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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)
B	d2yyeb1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	PurM N-terminal domain-like	PurM N-terminal domain-like	Selenide, water dikinase SelD	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
B	d2yyeb2	Alpha and beta proteins (a+b)	PurM C-terminal domain-like	PurM C-terminal domain-like	PurM C-terminal domain-like	Selenide, water dikinase SelD	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
B	d2yyeb3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
A	d2yyea1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	PurM N-terminal domain-like	PurM N-terminal domain-like	Selenide, water dikinase SelD	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
A	d2yyea2	Alpha and beta proteins (a+b)	PurM C-terminal domain-like	PurM C-terminal domain-like	PurM C-terminal domain-like	Selenide, water dikinase SelD	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
A	d2yyea3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	PurM N-terminal domain-like	8025575	4001523	SCOP2 (2022-06-29)
B	SCOP2 Family	PurM C-terminal domain-like	8025577	4002017	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	PurM N-terminal domain-like	8037954	3001759	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	PurM C-terminal domain-like	8037956	3000696	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	PurM C-terminal domain-like	8037956	3000696	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PurM N-terminal domain-like	8037954	3001759	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	GATase_2	e2yyeB1	A: alpha bundles	X: EGF-like	H: General secretion pathway protein M (EpsM) periplasmic domain-related	T: General secretion pathway protein M (EpsM) periplasmic domain-related	F: GATase_2	ECOD (develop294)
B	Ribonuc_L-PSP	e2yyeB2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Ribonuc_L-PSP	ECOD (develop294)
A	GATase_2	e2yyeA1	A: alpha bundles	X: EGF-like	H: General secretion pathway protein M (EpsM) periplasmic domain-related	T: General secretion pathway protein M (EpsM) periplasmic domain-related	F: GATase_2	ECOD (develop294)
A	Ribonuc_L-PSP	e2yyeA2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Ribonuc_L-PSP	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.1330.10	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
B	3.90.650.10	Alpha Beta	Alpha-Beta Complex	Phosphoribosyl-aminoimidazole Synthetase	Chain A, domain 2	CATH (4.3.0)
A	3.30.1330.10	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
A	3.90.650.10	Alpha Beta	Alpha-Beta Complex	Phosphoribosyl-aminoimidazole Synthetase	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02769	AIR synthase related protein, C-terminal domain (AIRS_C)	AIR synthase related protein, C-terminal domain	This family includes Hydrogen expression/formation protein HypE Swiss:P24193, AIR synthases Swiss:P08178 EC:6.3.3.1, FGAM synthase Swiss:P35852 EC:6.3.5.3 and selenide, water dikinase Swiss:P16456 EC:2.7.9.3. The function of the C-terminal domain of ...	This family includes Hydrogen expression/formation protein HypE Swiss:P24193, AIR synthases Swiss:P08178 EC:6.3.3.1, FGAM synthase Swiss:P35852 EC:6.3.5.3 and selenide, water dikinase Swiss:P16456 EC:2.7.9.3. The function of the C-terminal domain of AIR synthase is unclear, but the cleft formed between N and C domains is postulated as a sulphate binding site [1].	Domain
A, B	PF00586	AIR synthase related protein, N-terminal domain (AIRS)	AIR synthase related protein, N-terminal domain	This family includes Hydrogen expression/formation protein HypE Swiss:P24193, AIR synthases Swiss:P08178 EC:6.3.3.1, FGAM synthase Swiss:P35852 EC:6.3.5.3 and selenide, water dikinase Swiss:P16456 EC:2.7.9.3. The N-terminal domain of AIR synthase fo ...	This family includes Hydrogen expression/formation protein HypE Swiss:P24193, AIR synthases Swiss:P08178 EC:6.3.3.1, FGAM synthase Swiss:P35852 EC:6.3.5.3 and selenide, water dikinase Swiss:P16456 EC:2.7.9.3. The N-terminal domain of AIR synthase forms the dimer interface of the protein, and is suggested as a putative ATP binding domain [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Selenide, water dikinase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding phosphotransferase activity, paired acceptors selenide, water dikinase activity kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	oxoacid metabolic process modified amino acid biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process small molecule biosynthetic process carboxylic acid metabolic process modified amino acid metabolic process L-amino acid biosynthetic process primary metabolic process L-amino acid metabolic process oxoacid metabolic process modified amino acid biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process small molecule biosynthetic process carboxylic acid metabolic process modified amino acid metabolic process L-amino acid biosynthetic process primary metabolic process L-amino acid metabolic process selenocysteine metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process L-selenocysteine biosynthetic process alpha-amino acid biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036676	PurM-like, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR004536	Selenophosphate synthetase	Family
A, B	IPR010918	PurM-like, C-terminal domain	Domain
A, B	IPR023061	Selenophosphate synthetase, class I	Family
A, B	IPR016188	PurM-like, N-terminal domain	Domain
A, B	IPR036921	PurM-like, N-terminal domain superfamily	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.