Crystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase from Pectobacterium carotovorum

Experimental Data Snapshot

  • Resolution: 1.63 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report

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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: https://doi.org/10.1002/prot.25042
  • Primary Citation of Related Structures:  
    4Z9X, 4Z9Y, 4ZA2

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-deoxy-D-gluconate 3-dehydrogenase
A, B, C, D
253Pectobacterium carotovorum subsp. carotovorumMutation(s): 0 
Gene Names: RD01_02285RD02_01035
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.63 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.728α = 90
b = 72.655β = 90.81
c = 99.048γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
SCALEPACKdata reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Grants-in-aid from the Japan Society for the Promotion of ScienceJapan--
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  (Full details and data files)

  • Version 1.0: 2015-04-29
    Type: Initial release
  • Version 1.1: 2016-06-22
    Changes: Database references
  • Version 1.2: 2020-02-19
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description