Brand  (β version)

PDB ID: 4UU7

Hetero Atom Contents

  The number of atoms exceeds 100,000.
  So, it can not be displayed here.

Select unit:

Select hetatm:   

close
information
centroid:
interaction residue:

Select chain:   Sequence  

Data format:   

Color scheme of protein:

Ligands
Code Name Style Show Link
ZN Zinc ion PoSSuM
EDO 1,2-ethanediol PoSSuM
JO3 (2r)-2-methylbutanedioic acid PoSSuM
SUH (2s)-2-methylbutanedioic acid PoSSuM
Non-standard Residues
Code Name Show
Glycosylation
Code Name Emphasize
Modification
Code Name Show
BEZ Benzoic acid

Structure summary

Code : 4UU7   PDBj   RCSB PDB   PDBe
Header : HYDROLASE
Title : Crystal structure of zebrafish Sirtuin 5 in complex with 3-methyl- succinylated CPS1-peptide
Release Data : 2014-08-20
Compound :
mol_id molecule chains synonym
1 NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIAL A,B REGULATORY PROTEIN SIR2 HOMOLOG 5, SIRTUIN 5
ec: 3.5.1.-
fragment: CATALYTIC CORE, RESIDUES 30-298
mol_id molecule chains
2 CARBAMOYLPHOSPHATE SYNTHETASE I D
fragment: UNP RESIDUES 524-531
other_details: BENZOYLATED GLYCINE AT POSITION 1 3S-METHYL-SUCCINYL-LYSINE AND 3R-METHYL-SUCCINYL-LYSINE AT POSITION 4
Source :
mol_id organism_scientific organism_common expression_system
1 DANIO RERIO  (taxid:7955) ZEBRAFISH ESCHERICHIA COLI  (taxid:469008)
expression_system_strain: BL21(DE3)
expression_system_variant: CODONPLUS
expression_system_vector_type: PLASMID
expression_system_vector: PET151
mol_id organism_scientific organism_common
2 HOMO SAPIENS  (taxid:9606) HUMAN
synthetic: yes
Authors : Pannek, M., Gertz, M., Steegborn, C.
Keywords : HYDROLASE, SIRTUIN 5, REGULATORY ENZYME, DEACYLASE, MITOCHONDRIAL, ROSSMANN-FOLD, ZINC-BINDING
Exp. method : X-RAY DIFFRACTION ( 3.00 Å )
Citation :

Chemical Probing of the Human Sirtuin 5 Active Site Reveals its Substrate Acyl Specificity and Peptide-Based Inhibitors.

Roessler, C.,Nowak, T.,Pannek, M.  et al.
(2014)  Angew.Chem.Int.Ed.Engl.  53 : 10728

PubMed: 25111069
DOI: 10.1002/ANIE.201402679

Reaction

Chain : A, B
UniProt : Q6DHI5 (SIR5_DANRE)
Reaction: EC: Evidence:
Physiological Direction:
N(6)-malonyl-L-lysyl-[protein] + NAD(+) + H2O = 2''-O-malonyl- ADP-D-ribose + nicotinamide + L-lysyl-[protein] - HAMAP-Rule:MF_03160
-
N(6)-succinyl-L-lysyl-[protein] + NAD(+) + H2O = 2''-O- succinyl-ADP-D-ribose + nicotinamide + L-lysyl-[protein] - HAMAP-Rule:MF_03160
-
N(6)-glutaryl-L-lysyl-[protein] + NAD(+) + H2O = 2''-O- glutaryl-ADP-D-ribose + nicotinamide + L-lysyl-[protein] - HAMAP-Rule:MF_03160
-
Cofactor: Evidence: Note:
Zn(2+) ECO:0000255 | HAMAP-Rule:MF_03160
Binds 1 zinc ion per subunit.
Chain : D
UniProt : Q5R209 (Q5R209_HUMAN)
Reaction: EC: Evidence:
Physiological Direction:
hydrogencarbonate + NH4(+) + 2 ATP = carbamoyl phosphate + 2 ADP + phosphate + 2 H(+) 6.3.4.16 ARBA:ARBA00047359
-