1S5P | pdb_00001s5p

Structure and substrate binding properties of cobB, a Sir2 homolog protein deacetylase from Eschericia coli.

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	d1s5pa_	Alpha and beta proteins (a/b)	DHS-like NAD/FAD-binding domain	DHS-like NAD/FAD-binding domain	Sir2 family of transcriptional regulators	NAD-dependent deacetylase CobB	(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	SCOP2 Family	Sir2 family of transcriptional regulators	8029011	4003387	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DHS-like NAD/FAD-binding domain	8041390	3001728	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	SIR2_1st	e1s5pA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: SIR2_1st	ECOD (1.6)
A	PTZ00408	e1s5pA1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PTZ00408	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (4.3.0)
A	3.30.1600.10	Alpha Beta	2-Layer Sandwich	SIR2/SIRT2 'Small Domain'	SIR2/SIRT2 'Small Domain'	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02146	Sir2 family (SIR2)	Sir2 family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	NAD-dependent deacetylase	deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein acyltransferase activity histone H3K18 deacetylase activity, NAD-dependent deacylase activity histone deacetylase activity, NAD-dependent transferase activity NAD-dependent protein lysine deacylase activity histone deacetylase activity histone H3K deacetylase activity NAD-dependent protein lysine deacetylase activity acyltransferase activity, transferring groups other than amino-acyl groups catalytic activity deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein acyltransferase activity histone H3K18 deacetylase activity, NAD-dependent deacylase activity histone deacetylase activity, NAD-dependent transferase activity NAD-dependent protein lysine deacylase activity histone deacetylase activity histone H3K deacetylase activity NAD-dependent protein lysine deacetylase activity acyltransferase activity, transferring groups other than amino-acyl groups catalytic activity guanyl nucleotide binding binding cyclic nucleotide binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding cyclic-di-GMP binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein-malonyllysine demalonylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds histone H3K4 deacetylase activity, NAD-dependent NAD-dependent protein de-2-hydroxyisobutyrylase activity NAD+ binding NAD binding adenyl nucleotide binding protein-succinyllysine desuccinylase activity histone H3K56 deacetylase activity, NAD-dependent histone H3K9 deacetylase activity, NAD-dependent identical protein binding protein binding protein homodimerization activity protein dimerization activity histone H3K14 deacetylase activity, NAD-dependent lipoamidase activity cation binding transition metal ion binding zinc ion binding metal ion binding histone H4K16 deacetylase activity, NAD-dependent histone H4K deacetylase activity pentosyltransferase activity NAD+ poly-ADP-ribosyltransferase activity glycosyltransferase activity	chemotaxis response to stimulus taxis response to chemical response to external stimulus locomotion biological process involved in interspecies interaction between organisms response to other organism defense response response to biotic stimulus defense response to virus defense response to other organism response to stress response to external biotic stimulus chemotaxis response to stimulus taxis response to chemical response to external stimulus locomotion biological process involved in interspecies interaction between organisms response to other organism defense response response to biotic stimulus defense response to virus defense response to other organism response to stress response to external biotic stimulus response to virus	cellular anatomical structure intracellular anatomical structure cytoplasm
B	HISTONE H4 (RESIDUES 12-19)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR027546	Sirtuin, class III	Family
A	IPR026590	Sirtuin family, catalytic core domain	Domain
A	IPR003000	Sirtuin family	Family
A	IPR029035	DHS-like NAD/FAD-binding domain superfamily	Homologous Superfamily
A	IPR050134	NAD-dependent sirtuin protein deacylases	Family
A	IPR026591	Sirtuin, catalytic core small domain superfamily	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	ALY	Parent Component: LYS RESID: AA0055 PSI-MOD : N6-acetyl-L-lysine MOD:00064

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.