4O8A

First structure of a proline utilization A proline dehydrogenase domain

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)
A	d4o8aa1	All alpha proteins	N-terminal domain of bifunctional PutA protein	N-terminal domain of bifunctional PutA protein	N-terminal domain of bifunctional PutA protein	N-terminal domain of bifunctional PutA protein	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d4o8aa2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	FAD-linked oxidoreductase	Proline dehydrohenase domain of bifunctional PutA protein	Proline dehydrohenase domain of bifunctional PutA protein	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	N-terminal domain of bifunctional PutA protein	8030342	4002552	SCOP2 (2022-06-29)
A	SCOP2 Family	Proline dehydrogenase domain of bifunctional PutA protein	8030343	4002880	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	N-terminal domain of bifunctional PutA protein	8042721	3001406	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FAD-linked oxidoreductase	8042722	3000663	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)
A	Pro_dh	e4o8aA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Pro_dh	ECOD (1.6)
A	putA_2nd,Pro_dh-DNA_bdg	e4o8aA2	A: extended segments	X: N-terminal domain of bifunctional PutA protein (From Topology)	H: N-terminal domain of bifunctional PutA protein (From Topology)	T: N-terminal domain of bifunctional PutA protein	F: putA_2nd,Pro_dh-DNA_bdg	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.220	Alpha Beta	Alpha-Beta Barrel	TIM Barrel		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01619	Proline dehydrogenase (Pro_dh)	Proline dehydrogenase	-	Family
A	PF18327	Proline utilization A proline dehydrogenase N-terminal domain (PRODH)	Proline utilization A proline dehydrogenase N-terminal domain	This is the N-terminal domain found in Proline utilization A (PutA) proteins. Proline utilization A (PutA) is a flavoprotein that has mutually exclusive roles as a transcriptional repressor of the put regulon and a membrane-associated enzyme that cat ...	This is the N-terminal domain found in Proline utilization A (PutA) proteins. Proline utilization A (PutA) is a flavoprotein that has mutually exclusive roles as a transcriptional repressor of the put regulon and a membrane-associated enzyme that catalyzes the oxidation of proline to glutamate [4]. The N-terminal region carries the flavoenzyme proline dehydrogenase (PRODH) domain which catalyzes the 2-electron oxidation of proline with the concomitant reduction of a flavin cofactor [9].	Domain
A	PF14850	DNA-binding domain of Proline dehydrogenase (Pro_dh-DNA_bdg)	DNA-binding domain of Proline dehydrogenase	This domain lies at the N-terminus of bifunctional proline-dehydrogenases and is found to bind DNA.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Bifunctional protein PutA	flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding small molecule binding sequence-specific DNA binding DNA binding nucleic acid binding transcription regulator activity DNA-binding transcription repressor activity flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding small molecule binding sequence-specific DNA binding DNA binding nucleic acid binding transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding identical protein binding protein binding protein homodimerization activity protein dimerization activity 1-pyrroline-5-carboxylate dehydrogenase activity oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on the CH-NH group of donors proline dehydrogenase activity oxidoreductase activity, acting on the CH-NH group of donors, quinone or similar compound as acceptor	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process glutamine family amino acid biosynthetic process oxoacid metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process glutamine family amino acid metabolic process proline metabolic process small molecule metabolic process proline biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process proteinogenic amino acid biosynthetic process alpha-amino acid biosynthetic process catabolic process glutamine family amino acid catabolic process organic acid catabolic process proline catabolic process cellular catabolic process carboxylic acid catabolic process glutamate metabolic process amino acid catabolic process proline catabolic process to glutamate dicarboxylic acid metabolic process L-amino acid catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process small molecule catabolic process response to oxidative stress response to stimulus response to stress	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane cytoplasmic side of plasma membrane cytoplasmic side of membrane side of membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002872	Proline dehydrogenase domain	Domain
A	IPR015590	Aldehyde dehydrogenase domain	Domain
A	IPR048798	PutA, RHH domain	Domain
A	IPR016161	Aldehyde/histidinol dehydrogenase	Homologous Superfamily
A	IPR029041	FAD-linked oxidoreductase-like	Homologous Superfamily
A	IPR010985	Ribbon-helix-helix	Homologous Superfamily
A	IPR025703	Bifunctional protein PutA	Family
A	IPR013321	Arc-type ribbon-helix-helix	Homologous Superfamily
A	IPR029510	Aldehyde dehydrogenase, glutamic acid active site	Conserved Site
A	IPR024089	Proline dehydrogenase PutA, domain I/II	Homologous Superfamily
A	IPR016160	Aldehyde dehydrogenase, cysteine active site	Conserved Site
A	IPR024082	Proline dehydrogenase PutA, domain II	Domain
A	IPR016162	Aldehyde dehydrogenase, N-terminal	Homologous Superfamily
A	IPR041349	Proline utilization A proline dehydrogenase N-terminal domain	Domain
A	IPR050485	Proline metabolism enzyme	Family
A	IPR024090	Proline dehydrogenase PutA, domain I	Homologous Superfamily
A	IPR016163	Aldehyde dehydrogenase, C-terminal	Homologous Superfamily
A	IPR005933	Bifunctional protein PutA, C-terminal domain	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.