Structure of PDB 5ten Chain E

Receptor sequence

>5tenE (length=269) Species: 216895 (Vibrio vulnificus CMCP6)

MVRIAVAGAAGRMGRNLVKAAHHNPVAKVAAGSERPESSLVGVDLGELCG
EGKFDVVVCDDLAKQIDQFDVIIDFTAPASTLNNLALCQQYGKSIVIGTT
GFTEEQREQIDLVAQQVPVVMAPNYSVGVNLVFKLLEKAAKVMGDYCDIE
IVEAHHRHKVDAPSGTAIGMGEAIAGAMGNKLSDVAVYAREGITGERTKD
EIGFATIRAGDIVGEHTAMFADIGERVEITHKATDRMTFANGAVKAAVWL
HEKPAGFYTMTDVLGLNDL

3D structure

• PDB: 5ten Comparative structural and mechanistic studies of 4-hydroxy-tetrahydrodipicolinate reductases from Mycobacterium tuberculosis and Vibrio vulnificus.
• Chain: E
• Resolution: 2.45 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H155 K159
• Catalytic site (residue number reindexed from 1): H155 K159
• Enzyme Commision number: 1.17.1.8: 4-hydroxy-tetrahydrodipicolinate reductase.

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	NAD	E	G8 G11 R12 M13 E34 F75 T76 S80 G98 T100 P123 Y125 F239	G8 G11 R12 M13 E34 F75 T76 S80 G98 T100 P123 Y125 F239
BS02	7FN	E	T100 H155 H156 K159 G165 T166	T100 H155 H156 K159 G165 T166

Gene Ontology

Molecular Function

• GO:0008839 4-hydroxy-tetrahydrodipicolinate reductase
• GO:0016491 oxidoreductase activity
• GO:0016726 oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor
• GO:0050661 NADP binding
• GO:0051287 NAD binding

Biological Process

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

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:5ten, PDBe:5ten, PDBj:5ten
• PDBsum: 5ten
• PubMed: 32980502
• UniProt: Q8DEM0|DAPB_VIBVU 4-hydroxy-tetrahydrodipicolinate reductase (Gene Name=dapB)