ISDA

Deposition Date 2010-07-06

Release Date 2011-04-20

Last Version Date 2023-11-01

Entry Detail

PDB ID:

3NUG

Keywords:

OXIDOREDUCTASE

Title:

Crystal structure of wild type tetrameric pyridoxal 4-dehydrogenase from Mesorhizobium loti

Biological Source:

Source Organism:

Mesorhizobium loti (Taxon ID: 381)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.79 Å

R-Value Free:

0.20

R-Value Work:

0.15

R-Value Observed:

0.15

Space Group:

P 1 21 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:3-oxoacyl-(Acyl-carrier protein) reductase
Gene (Uniprot):pldh-t
Chain IDs:A, B, C, D
Chain Length:247
Number of Molecules:4
Biological Source:Mesorhizobium loti

UniProt ID:Q988B7 Pfam ID:PF13561 EC:1.1.1.107

Ligand Molecules

ACY

NAD

Primary Citation

The crystal structure of SDR-type pyridoxal 4-dehydrogenase of Mesorhizobium loti

Chu, H.N, Kobayashi, J, Mikami, B, Yagi, T, Chu, H.N, Kobayashi, J, Yoshikane, Y, Mikami, B, Yagi, T.Show

Biosci.Biotechnol.Biochem. 75 388 390 (2011)

PMID: 21307574 DOI: 10.1271/bbb.100748

Abstact

Pyridoxal 4-dehydrogenase catalyzes the irreversible oxidation of pyridoxal to 4-pyridoxolactone and is involved in degradation pathway I of pyridoxine, a vitamin B(6) compound. Its crystal structure was elucidated for the first time. Molecular replacement with (S)-1-phenylthanol dehydrogenase (PDB code 2EW8) was adopted to determine the tertiary structure of the NAD(+)-bound enzyme.

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Primary Citation of related structures