2AMF | pdb_00002amf

Crystal structure of 1-Pyrroline-5-Carboxylate Reductase from Human Pathogen Streptococcus Pyogenes

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)
C	d2amfc1	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	ProC C-terminal domain-like	Pyrroline-5-carboxylate reductase ProC	(Streptococcus pyogenes M1 GAS ) [TaxId: 160490 ],	SCOPe (2.08)
C	d2amfc2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	6-phosphogluconate dehydrogenase-like, N-terminal domain	Pyrroline-5-carboxylate reductase ProC	(Streptococcus pyogenes M1 GAS ) [TaxId: 160490 ],	SCOPe (2.08)
E	d2amfe1	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	ProC C-terminal domain-like	Pyrroline-5-carboxylate reductase ProC	(Streptococcus pyogenes M1 GAS ) [TaxId: 160490 ],	SCOPe (2.08)
E	d2amfe2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	6-phosphogluconate dehydrogenase-like, N-terminal domain	Pyrroline-5-carboxylate reductase ProC	(Streptococcus pyogenes M1 GAS ) [TaxId: 160490 ],	SCOPe (2.08)
E	d2amfe3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Streptococcus pyogenes M1 GAS ) [TaxId: 160490 ],	SCOPe (2.08)
D	d2amfd1	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	ProC C-terminal domain-like	Pyrroline-5-carboxylate reductase ProC	(Streptococcus pyogenes M1 GAS ) [TaxId: 160490 ],	SCOPe (2.08)
D	d2amfd2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	6-phosphogluconate dehydrogenase-like, N-terminal domain	Pyrroline-5-carboxylate reductase ProC	(Streptococcus pyogenes M1 GAS ) [TaxId: 160490 ],	SCOPe (2.08)
D	d2amfd3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Streptococcus pyogenes M1 GAS ) [TaxId: 160490 ],	SCOPe (2.08)
B	d2amfb1	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	ProC C-terminal domain-like	Pyrroline-5-carboxylate reductase ProC	(Streptococcus pyogenes M1 GAS ) [TaxId: 160490 ],	SCOPe (2.08)
B	d2amfb2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	6-phosphogluconate dehydrogenase-like, N-terminal domain	Pyrroline-5-carboxylate reductase ProC	(Streptococcus pyogenes M1 GAS ) [TaxId: 160490 ],	SCOPe (2.08)
B	d2amfb3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Streptococcus pyogenes M1 GAS ) [TaxId: 160490 ],	SCOPe (2.08)
A	d2amfa1	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	ProC C-terminal domain-like	Pyrroline-5-carboxylate reductase ProC	(Streptococcus pyogenes M1 GAS ) [TaxId: 160490 ],	SCOPe (2.08)
A	d2amfa2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	6-phosphogluconate dehydrogenase-like, N-terminal domain	Pyrroline-5-carboxylate reductase ProC	(Streptococcus pyogenes M1 GAS ) [TaxId: 160490 ],	SCOPe (2.08)
A	d2amfa3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Streptococcus pyogenes M1 GAS ) [TaxId: 160490 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	6-phosphogluconate dehydrogenase-like	8058540	3000048	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	6-phosphogluconate dehydrogenase-like	8058540	3000048	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	6-phosphogluconate dehydrogenase-like	8058540	3000048	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	6-phosphogluconate dehydrogenase-like	8058540	3000048	SCOP2B (2022-06-29)
A	SCOP2 Family	Pyrroline-5-carboxylate reductase (ProC)-like	8058539	4000113	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	6-phosphogluconate dehydrogenase-like	8058540	3000048	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C		e2amfC1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F:	ECOD (v294.1)
C	FAD_binding_3	e2amfC2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (v294.1)
E		e2amfE1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F:	ECOD (v294.1)
E	FAD_binding_3	e2amfE2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (v294.1)
D		e2amfD1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F:	ECOD (v294.1)
D	FAD_binding_3	e2amfD2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (v294.1)
B		e2amfB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F:	ECOD (v294.1)
B	FAD_binding_3	e2amfB2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (v294.1)
A		e2amfA1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F:	ECOD (v294.1)
A	FAD_binding_3	e2amfA2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	1.10.3730.10	Mainly Alpha	Orthogonal Bundle	ProC C-terminal domain-like fold	ProC C-terminal domain-like	CATH (4.3.0)
E	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
E	1.10.3730.10	Mainly Alpha	Orthogonal Bundle	ProC C-terminal domain-like fold	ProC C-terminal domain-like	CATH (4.3.0)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	1.10.3730.10	Mainly Alpha	Orthogonal Bundle	ProC C-terminal domain-like fold	ProC C-terminal domain-like	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	1.10.3730.10	Mainly Alpha	Orthogonal Bundle	ProC C-terminal domain-like fold	ProC C-terminal domain-like	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	1.10.3730.10	Mainly Alpha	Orthogonal Bundle	ProC C-terminal domain-like fold	ProC C-terminal domain-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E	PF14748	Pyrroline-5-carboxylate reductase dimerisation (P5CR_dimer)	Pyrroline-5-carboxylate reductase dimerisation	Pyrroline-5-carboxylate reductase consists of two domains, an N-terminal catalytic domain (Pfam:PF03807) and a C-terminal dimerisation domain. This is the dimerisation domain [1].	Domain
A, B, C, D, E	PF03807	NADP oxidoreductase coenzyme F420-dependent (F420_oxidored)	NADP oxidoreductase coenzyme F420-dependent	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E	1-Pyrroline-5-Carboxylate reductase	oxidoreductase activity oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on the CH-NH group of donors pyrroline-5-carboxylate reductase activity catalytic activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding	oxoacid metabolic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process amino acid metabolic process primary metabolic process L-proline biosynthetic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process L-glutamine family amino acid biosynthetic process L-amino acid metabolic process carboxylic acid biosynthetic process proteinogenic amino acid metabolic process amino acid biosynthetic process oxoacid metabolic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process amino acid metabolic process primary metabolic process L-proline biosynthetic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process L-glutamine family amino acid biosynthetic process L-amino acid metabolic process carboxylic acid biosynthetic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process L-proline metabolic process metabolic process cellular process small molecule metabolic 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, C, D, E	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D, E	IPR000304	Pyrroline-5-carboxylate reductase-like	Family
A, B, C, D, E	IPR008927	6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E	IPR029036	Pyrroline-5-carboxylate reductase, dimerisation domain	Domain
A, B, C, D, E	IPR028939	Pyrroline-5-carboxylate reductase, catalytic, N-terminal	Domain

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.