Het-PDB Navi2 (PDB: 4F56)

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Ligands
Code	Name		Style	Show	Link
ZN	Zinc ion				PoSSuM
CGK	3-[(2r,3ar,5r,6r,6ar)-5-({[(S)-{[(S)-{[(2r,3s,4r,5r)-5-(6-amino-9h-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-2,6-dihydroxytetrahydrofuro[2,3-D][1,3]oxathiol-2-yl]propanoic acid				PoSSuM

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Download interaction data: 4F56

Code :

4F56 PDBj RCSB PDB PDBe

Header :

HYDROLASE

Title :

The bicyclic intermediate structure provides insights into the desuccinylation mechanism of SIRT5

Release Data :

2012-06-20

Compound :

mol_id	molecule	chains	synonym
1	NAD-dependent lysine demalonylase and desuccinylase sirtuin-5, mitochondrial	A,B	SIR2-like protein 5
	ec: 3.5.1.- fragment: UNP Residue 34-302

mol_id	molecule	chains	synonym
2	peptide from Histone H3.1	C,D	Histone H3/a, Histone H3/b, Histone H3/c, Histone H3/d, Histone H3/f, Histone H3/h, Histone H3/i, Histone H3/j, Histone H3/k, Histone H3/l
	fragment: UNP residue 5-16

Source :

mol_id	organism_scientific	organism_common	expression_system
1	Homo sapiens (taxid:9606)	Human	Escherichia coli (taxid:562)
	gene: SIR2L5, SIRT5 expression_system_strain: BL21 R2 expression_system_vector_type: plasmid expression_system_plasmid: pDEST-F1

mol_id	organism_scientific	organism_common
2	Homo sapiens (taxid:9606)	Human
	synthetic: yes

Authors :

Zhou, Y., Hao, Q.

Keywords :

Zn-binding domain, Rossmann fold domain, NAD-dependent demalonylase and desuccinylase, mitochondrial sirtuin, HYDROLASE

Exp. method :

X-RAY DIFFRACTION ( 1.7000 Å )

Citation :

The Bicyclic Intermediate Structure Provides Insights into the Desuccinylation Mechanism of Human Sirtuin 5 (SIRT5)

Zhou, Y.,Zhang, H.,He, B. et al.
(2012) J.Biol.Chem. 287 : 28307 - 28314

Chain :

A, B

UniProt :

Q9NXA8 (SIR5_HUMAN)

Reaction:	EC:	Evidence:
Reaction:	Physiological Direction:	Evidence:
H2O + N(6)-malonyl-L-lysyl-[protein] + NAD(+) = 2''-O-malonyl- ADP-D-ribose + L-lysyl-[protein] + nicotinamide	-	HAMAP-Rule:MF_03160, PubMed:22076378
	-	HAMAP-Rule:MF_03160, PubMed:22076378
H2O + N(6)-succinyl-L-lysyl-[protein] + NAD(+) = 2''-O- succinyl-ADP-D-ribose + L-lysyl-[protein] + nicotinamide	-	HAMAP-Rule:MF_03160, PubMed:22076378, PubMed:29180469
	-	HAMAP-Rule:MF_03160, PubMed:22076378, PubMed:29180469
H2O + N(6)-glutaryl-L-lysyl-[protein] + NAD(+) = 2''-O- glutaryl-ADP-D-ribose + L-lysyl-[protein] + nicotinamide	-	HAMAP-Rule:MF_03160, PubMed:24703693
	-	HAMAP-Rule:MF_03160, PubMed:24703693

PDB ID: 4F56