Structure of PDB 3d81 Chain A

Receptor sequence

>3d81A (length=235) Species: 2336 (Thermotoga maritima)

MKMKEFLDLLNESRLTVTLTGAGISTPSGIPDFQNVFDIDFFYSHPEEFY
RFAKEGIFPMLQAKPNLAHVLLAKLEEKGLIEAVITQNIDRLHQRAGSKK
VIELHGNVEEYYCVRCEKKYTVEDVIKKLESSDVPLCDDCNSLIRPNIVF
FGENLPQDALREAIGLSSRASLMIVLGSSLVVYPAAELPLITVRSGGKLV
IVNLGETPFDDIATLKYNMDVVEFARRVMEEGGIS

3D structure

• PDB: 3d81 Structural insights into intermediate steps in the Sir2 deacetylation reaction.
• Chain: A
• Resolution: 2.5 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): P31 D32 F33 N99 D101 H116
• Catalytic site (residue number reindexed from 1): P31 D32 F33 N88 D90 H105
• Enzyme Commision number: 2.3.1.286: protein acetyllysine N-acetyltransferase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	peptide	A	G21 A22 G23 T26 D32 F33 Q98 H116 I159 V160 F161 F162 G163 E164 N165 L166 G188 S189 S190 V192 V193 Y194 N214 L215 D231 V232	G21 A22 G23 T26 D32 F33 Q87 H105 I148 V149 F150 F151 G152 E153 N154 L155 G177 S178 S179 V181 V182 Y183 N203 L204 D220 V221
BS02	ZN	A	C124 C127 C148	C113 C116 C137

Gene Ontology

Molecular Function

• GO:0008270 zinc ion binding
• GO:0016740 transferase activity
• GO:0017136 NAD-dependent histone deacetylase activity
• GO:0034979 NAD-dependent protein lysine deacetylase activity
• GO:0046872 metal ion binding
• GO:0051287 NAD binding
• GO:0070403 NAD+ binding

Biological Process

• GO:0006338 chromatin remodeling
• GO:0006476 protein deacetylation

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:3d81, PDBe:3d81, PDBj:3d81
• PDBsum: 3d81
• PubMed: 18786399
• UniProt: Q9WYW0|NPD_THEMA NAD-dependent protein deacetylase (Gene Name=cobB)