Structure of PDB 1npd Chain A

Receptor sequence

>1npdA (length=287) Species: 562 (Escherichia coli)

MDVTAKYELIGLMAYPIRHSLSPEMQNKALEKAGLPFTYMAFEVDNDSFP
GAIEGLKALKMRGTGVSMPNKQLACEYVDELTPAAKLVGAINTIVNDDGY
LRGYNTDGTGHIRAIKESGFDIKGKTMVLLGAGGASTAIGAQGAIEGLKE
IKLFNRRDEFFDKALAFAQRVNENTDCVVTVTDLADQQAFAEALASADIL
TNGTKVGMKPLENESLVNDISLLHPGLLVTECVYNPHMTKLLQQAQQAGC
KTIDGYGMLLWQGAEQFTLWTGKDFPLEYVKQVMGFG

3D structure

• PDB: 1npd The 2.3-A crystal structure of the shikimate 5-dehydrogenase orthologue YdiB from Escherichia coli suggests a novel catalytic environment for an NAD-dependent dehydrogenase
• Chain: A
• Resolution: 2.3 Å

Enzymatic activity

• Enzyme Commision number: 1.1.1.282: quinate/shikimate dehydrogenase [NAD(P)(+)].

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	A	G133 G134 A135 N155 R156 D158 F160 T204 K205 V206 M208 C232 Y234 M258 L259	G133 G134 A135 N155 R156 D158 F160 T204 K205 V206 M208 C232 Y234 M258 L259

Gene Ontology

Molecular Function

• GO:0004764 shikimate 3-dehydrogenase (NADP+) activity
• GO:0005515 protein binding
• GO:0016491 oxidoreductase activity
• GO:0030266 quinate 3-dehydrogenase (NAD+) activity
• GO:0042803 protein homodimerization activity
• GO:0052733 quinate 3-dehydrogenase (NADP+) activity
• GO:0052734 shikimate 3-dehydrogenase (NAD+) activity

Biological Process

• GO:0008652 amino acid biosynthetic process
• GO:0009073 aromatic amino acid family biosynthetic process
• GO:0009423 chorismate biosynthetic process
• GO:0019632 shikimate metabolic process

External links

• PDB: RCSB:1npd, PDBe:1npd, PDBj:1npd
• PDBsum: 1npd
• PubMed: 12624088
• UniProt: P0A6D5|YDIB_ECOLI Quinate/shikimate dehydrogenase (Gene Name=ydiB)