4W7I

Crystal structure of DEH reductase A1-R' mutant

  • Classification: OXIDOREDUCTASE
  • Organism(s): Sphingomonas sp. A1
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2014-08-22 Released: 2014-09-24 
  • Deposition Author(s): Takase, R., Mikami, B., Kawai, S., Murata, K., Hashimoto, W.
  • Funding Organization(s): Grants-in-Aid for Scientific Research from Japan Society for the Promotion of Science, 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 Japan Society for the Promotion of Science for Young Scientists

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure-based Conversion of the Coenzyme Requirement of a Short-chain Dehydrogenase/Reductase Involved in Bacterial Alginate Metabolism.

Takase, R.Mikami, B.Kawai, S.Murata, K.Hashimoto, W.

(2014) J Biol Chem 289: 33198-33214

  • DOI: 10.1074/jbc.M114.585661
  • Primary Citation of Related Structures:  
    4TKL, 4TKM, 4W7H, 4W7I

  • PubMed Abstract: 
  • The alginate-assimilating bacterium, Sphingomonas sp. strain A1, degrades the polysaccharides to monosaccharides through four alginate lyase reactions. The resultant monosaccharide, which is nonenzymatically converted to 4-deoxy-L-erythro-5-hexoseulose uronate (DEH), is further metabolized to 2-keto-3-deoxy-D-gluconate by NADPH-dependent reductase A1-R in the short-chain dehydrogenase/reductase (SDR) family ...

    The alginate-assimilating bacterium, Sphingomonas sp. strain A1, degrades the polysaccharides to monosaccharides through four alginate lyase reactions. The resultant monosaccharide, which is nonenzymatically converted to 4-deoxy-L-erythro-5-hexoseulose uronate (DEH), is further metabolized to 2-keto-3-deoxy-D-gluconate by NADPH-dependent reductase A1-R in the short-chain dehydrogenase/reductase (SDR) family. A1-R-deficient cells produced another DEH reductase, designated A1-R', with a preference for NADH. Here, we show the identification of a novel NADH-dependent DEH reductase A1-R' in strain A1, structural determination of A1-R' by x-ray crystallography, and structure-based conversion of a coenzyme requirement in SDR enzymes, A1-R and A1-R'. A1-R' was purified from strain A1 cells and enzymatically characterized. Except for the coenzyme requirement, there was no significant difference in enzyme characteristics between A1-R and A1-R'. Crystal structures of A1-R' and A1-R'·NAD(+) complex were determined at 1.8 and 2.7 Å resolutions, respectively. Because of a 64% sequence identity, overall structures of A1-R' and A1-R were similar, although a difference in the coenzyme-binding site (particularly the nucleoside ribose 2' region) was observed. Distinct from A1-R, A1-R' included a negatively charged, shallower binding site. These differences were caused by amino acid residues on the two loops around the site. The A1-R' mutant with the two A1-R-typed loops maintained potent enzyme activity with specificity for NADPH rather than NADH, demonstrating that the two loops determine the coenzyme requirement, and loop exchange is a promising method for conversion of coenzyme requirement in the SDR family.


    Organizational Affiliation

    From the Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, and whasimot@kais.kyoto-u.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
4-deoxy-L-erythro-5-hexoseulose uronate reductase A1-R'A, B, C, D258Sphingomonas sp. A1Mutation(s): 0 
UniProt
Find proteins for A0A096LNF1 (Sphingomonas sp. A1)
Explore A0A096LNF1 
Go to UniProtKB:  A0A096LNF1
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.215α = 90
b = 178.152β = 111.76
c = 96.013γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Grants-in-Aid for Scientific Research from 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 Japan Society for the Promotion of Science for Young ScientistsJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-24
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Database references
  • Version 1.2: 2020-01-29
    Changes: Data collection, Database references, Derived calculations, Other, Source and taxonomy