Structure of PDB 5vo3 Chain A

Receptor sequence

>5vo3A (length=380) Species: 727 (Haemophilus influenzae)

ASNAMKEKVVSLAQDLIRRPSISPNDEGCQQIIAERLEKLGFQIEWMPFN
DTLNLWAKHGTSEPVIAFAGHTDVVPTGDENQWSSPPFSAEIIDGMLYGR
GAADMKGSLAAMIVAAEEYVKANPNHKGTIALLITSDEEATAKDGTIHVV
ETLMARDEKITYCMVGEPSSAKNLGDVVKNGRRGSITGNLYIQGIQGHVA
YPHLAENPIHKAALFLQELTTYQWDKGNEFFPPTSLQIANIHAGTGSNNV
IPAELYIQFNLRYCTEVTDEIIKQKVAEMLEKHNLKYRIEWNLSGKPFLT
KPGKLLDSITSAIEETIGITPKAETGGGTSDGRFIALMGAEVVEFGPLNS
TIHKVNECVSVEDLGKCGEIYHKMLVNLLD

3D structure

• PDB: 5vo3 Structural Evidence of a Major Conformational Change Triggered by Substrate Binding in DapE Enzymes: Impact on the Catalytic Mechanism.
• Chain: A
• Resolution: 1.954 Å

Enzymatic activity

• Enzyme Commision number: 3.5.1.18: succinyl-diaminopimelate desuccinylase.

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	SIN	A	D100 E134 E135 E163 R178 G324 T325 H349	D104 E138 E139 E167 R182 G328 T329 H353
BS02	API	A	E134 E135 A136 S181 R258 S290 G324 T325	E138 E139 A140 S185 R262 S294 G328 T329
BS03	ZN	A	H67 D100 E163	H71 D104 E167
BS04	ZN	A	D100 E135 H349	D104 E139 H353

Gene Ontology

Molecular Function

• GO:0008270 zinc ion binding
• GO:0009014 succinyl-diaminopimelate desuccinylase activity
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding
• GO:0050897 cobalt ion binding

Biological Process

• GO:0009085 lysine biosynthetic process
• GO:0009089 lysine biosynthetic process via diaminopimelate
• GO:0019877 diaminopimelate biosynthetic process

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:5vo3, PDBe:5vo3, PDBj:5vo3
• PDBsum: 5vo3
• PubMed: 29272107
• UniProt: P44514|DAPE_HAEIN Succinyl-diaminopimelate desuccinylase (Gene Name=dapE)