4ZA2

Crystal structure of Pectobacterium carotovorum 2-keto-3-deoxy-D-gluconate dehydrogenase complexed with NAD+

  • Classification: OXIDOREDUCTASE
  • Expression System: Escherichia coli BL21(DE3)

  • Deposited: 2015-04-13 Released: 2015-04-29 
  • Deposition Author(s): Takase, R., Maruyama, Y., Oiki, S., Mikami, B., Murata, K., Hashimoto, W.
  • Funding Organization(s): Grants-in-aid from the Japan Society for the Promotion of Scienc; Promotion of Basic Research Activities for Innovative Biosciences (PROBRAIN) of Japan; Targeted Proteins Research Program from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of Japan; Research fellowships from the Japan Society for the Promotion of Science for Young Scientists 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural determinants in bacterial 2-keto-3-deoxy-D-gluconate dehydrogenase KduD for dual-coenzyme specificity

Takase, R.Maruyama, Y.Oiki, S.Mikami, B.Murata, K.Hashimoto, W.

(2016) Proteins 84: 934-947

  • DOI: 10.1002/prot.25042
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Short-chain dehydrogenase/reductase (SDR) is distributed in many organisms, from bacteria to humans, and has significant roles in metabolism of carbohydrates, lipids, amino acids, and other biomolecules. An important intermediate in acidic polysaccha ...

    Short-chain dehydrogenase/reductase (SDR) is distributed in many organisms, from bacteria to humans, and has significant roles in metabolism of carbohydrates, lipids, amino acids, and other biomolecules. An important intermediate in acidic polysaccharide metabolism is 2-keto-3-deoxy-d-gluconate (KDG). Recently, two short and long loops in Sphingomonas KDG-producing SDR enzymes (NADPH-dependent A1-R and NADH-dependent A1-R') involved in alginate metabolism were shown to be crucial for NADPH or NADH coenzyme specificity. Two SDR family enzymes-KduD from Pectobacterium carotovorum (PcaKduD) and DhuD from Streptococcus pyogenes (SpyDhuD)-prefer NADH as coenzyme, although only PcaKduD can utilize both NADPH and NADH. Both enzymes reduce 2,5-diketo-3-deoxy-d-gluconate to produce KDG. Tertiary and quaternary structures of SpyDhuD and PcaKduD and its complex with NADH were determined at high resolution (approximately 1.6 Å) by X-ray crystallography. Both PcaKduD and SpyDhuD consist of a three-layered structure, α/β/α, with a coenzyme-binding site in the Rossmann fold; similar to enzymes A1-R and A1-R', both arrange the two short and long loops close to the coenzyme-binding site. The primary structures of the two loops in PcaKduD and SpyDhuD were similar to those in A1-R' but not A1-R. Charge neutrality and moderate space at the binding site of the nucleoside ribose 2' coenzyme region were determined to be structurally crucial for dual-coenzyme specificity in PcaKduD by structural comparison of the NADH- and NADPH-specific SDR enzymes. The corresponding site in SpyDhuD was negatively charged and spatially shallow. This is the first reported study on structural determinants in SDR family KduD related to dual-coenzyme specificity. Proteins 2016; 84:934-947. © 2016 Wiley Periodicals, Inc.


    Organizational Affiliation

    Laboratory of Basic and Applied Molecular Biotechnology Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan.,Laboratory of Applied Structural Biology Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-deoxy-D-gluconate 3-dehydrogenase
A, B, C, D
253N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download SDF File 
Download CCD File 
D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 68.663α = 90.00
b = 72.654β = 90.81
c = 98.991γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALEPACKdata reduction
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Grants-in-aid from the Japan Society for the Promotion of SciencJapan--
Promotion of Basic Research Activities for Innovative Biosciences (PROBRAIN) of JapanJapan--
Targeted Proteins Research Program from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of JapanJapan--
Research fellowships from the Japan Society for the Promotion of Science for Young ScientistsJapan--

Revision History 

  • Version 1.0: 2015-04-29
    Type: Initial release
  • Version 1.1: 2016-06-22
    Type: Database references