2UYN

Crystal structure of E. coli TdcF with bound 2-ketobutyrate

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2uyna_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2uync_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2uynb_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	YjgF-like	8059829	3001733	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	YjgF-like	8059829	3001733	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	YjgF-like	8059829	3001733	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)
A	Ribonuc_L-PSP	e2uynA1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
C	Ribonuc_L-PSP	e2uynC1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
B	Ribonuc_L-PSP	e2uynB1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
C	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
B	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01042	Endoribonuclease L-PSP (Ribonuc_L-PSP)	Endoribonuclease L-PSP	Endoribonuclease active on single-stranded mRNA. Inhibits protein synthesis by cleavage of mRNA [1]. Previously thought to inhibit protein synthesis initiation [2]. This protein may also be involved in the regulation of purine biosynthesis [3]. Yjg ...	Endoribonuclease active on single-stranded mRNA. Inhibits protein synthesis by cleavage of mRNA [1]. Previously thought to inhibit protein synthesis initiation [2]. This protein may also be involved in the regulation of purine biosynthesis [3]. YjgF (renamed RidA) family members are enamine/imine deaminases. They hydrolyze reactive intermediates released by PLP-dependent enzymes, including threonine dehydratase [5]. YjgF also prevents inhibition of transaminase B (IlvE) in Salmonella [4].	Domain
B, C	PF01042	Endoribonuclease L-PSP (Ribonuc_L-PSP)	Endoribonuclease L-PSP	Endoribonuclease active on single-stranded mRNA. Inhibits protein synthesis by cleavage of mRNA [1]. Previously thought to inhibit protein synthesis initiation [2]. This protein may also be involved in the regulation of purine biosynthesis [3]. Yjg ...	Endoribonuclease active on single-stranded mRNA. Inhibits protein synthesis by cleavage of mRNA [1]. Previously thought to inhibit protein synthesis initiation [2]. This protein may also be involved in the regulation of purine biosynthesis [3]. YjgF (renamed RidA) family members are enamine/imine deaminases. They hydrolyze reactive intermediates released by PLP-dependent enzymes, including threonine dehydratase [5]. YjgF also prevents inhibition of transaminase B (IlvE) in Salmonella [4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	PROTEIN TDCF	hydrolase activity deaminase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds identical protein binding protein binding binding	oxoacid metabolic process aspartate family amino acid 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 proteinogenic amino acid metabolic process threonine metabolic process metabolic process cellular process small molecule metabolic process catabolic process oxoacid metabolic process aspartate family amino acid 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 proteinogenic amino acid metabolic process threonine metabolic process metabolic process cellular process small molecule metabolic process catabolic process short-chain fatty acid metabolic process organic acid catabolic process cellular catabolic process carboxylic acid catabolic process threonine catabolic process amino acid catabolic process propionate metabolic process fatty acid metabolic process aspartate family amino acid catabolic process L-amino acid catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process L-threonine catabolic process to propionate monocarboxylic acid metabolic process small molecule catabolic process lipid metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
B, C	PROTEIN TDCF	hydrolase activity deaminase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds identical protein binding protein binding binding	oxoacid metabolic process aspartate family amino acid 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 proteinogenic amino acid metabolic process threonine metabolic process metabolic process cellular process small molecule metabolic process catabolic process oxoacid metabolic process aspartate family amino acid 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 proteinogenic amino acid metabolic process threonine metabolic process metabolic process cellular process small molecule metabolic process catabolic process short-chain fatty acid metabolic process organic acid catabolic process cellular catabolic process carboxylic acid catabolic process threonine catabolic process amino acid catabolic process propionate metabolic process fatty acid metabolic process aspartate family amino acid catabolic process L-amino acid catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process L-threonine catabolic process to propionate monocarboxylic acid metabolic process small molecule catabolic process lipid metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR019897	RidA, conserved site	Conserved Site
A	IPR006056	RidA family	Family
A	IPR035959	RutC-like superfamily	Homologous Superfamily
A	IPR006175	YjgF/YER057c/UK114 family	Family
B, C	IPR019897	RidA, conserved site	Conserved Site
B, C	IPR006056	RidA family	Family
B, C	IPR035959	RutC-like superfamily	Homologous Superfamily
B, C	IPR006175	YjgF/YER057c/UK114 family	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	KCX	Parent Component: LYS
A	OCS	Parent Component: CYS RESID: AA0556 PSI-MOD : L-cysteic acid (L-cysteine sulfonic acid) MOD:00460
B, C	OCS	Parent Component: CYS RESID: AA0556 , AA0556 PSI-MOD : L-cysteic acid (L-cysteine sulfonic acid) MOD:00460 , L-cysteic acid (L-cysteine sulfonic acid) MOD:00460

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.