5KRV | pdb_00005krv

1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus in complex Arginine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.215 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structural characterization of 1-deoxy-D-xylulose 5-phosphate Reductoisomerase from Vibrio vulnificus.

Ussin, N.K.Bagnell, A.M.Offermann, L.R.Abdulsalam, R.Perdue, M.L.Magee, P.Chruszcz, M.

(2018) Biochim Biophys Acta Proteins Proteom 1866: 1209-1215

  • DOI: https://doi.org/10.1016/j.bbapap.2018.09.008
  • Primary Citation Related Structures: 
    5KQO, 5KRR, 5KRV, 5KRY, 5KS1

  • PubMed Abstract: 

    Vibrio vulnificus, a gram-negative bacterium, is the leading cause of seafood-borne illnesses and mortality in the United States. Previous studies have identified metabolites 2-C-methylerythritol 4-phosphate (MEP) as being essential for V. vulnificus growth and function. It was shown that 1-deoxy-D-xylulose-5-phosphate reductoisomerase (Dxr) is a critical enzyme in the viability of V. vulnificus, and many other bacteria, as it catalyzes the rearrangement of 1-deoxy-D-xylulose-5-phosphate (Dxp) to 2-C-methylerythritol 4-phosphate (MEP) within the MEP pathway, found in plants and bacteria. The MEP pathway produces the isoprenoids, isopentenyl diphosphate and dimethylallyl pyrophosphate. In this study, we produced and structurally characterized V. vulnificus Dxr. The enzyme forms a dimeric assembly and contains a metal ion in the active site. Protein produced in Escherichia coli co-purifies with Mg 2+ ions, however the Mg 2+ cations may be substituted with Mn 2+ , as both of these metals may be utilized by Dxrs. These findings will provide a basis for the design of Dxr inhibitors that may find application as antimicrobial compounds.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States.

Macromolecule Content 

  • Total Structure Weight: 93.34 kDa 
  • Atom Count: 6,155 
  • Modeled Residue Count: 787 
  • Deposited Residue Count: 854 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
1-deoxy-D-xylulose 5-phosphate reductoisomerase
A, B
427Vibrio vulnificus CMCP6Mutation(s): 0 
Gene Names: dxrVV1_1866
EC: 1.1.1.267
UniProt
Find proteins for Q8DBF5 (Vibrio vulnificus (strain CMCP6))
Explore Q8DBF5 
Go to UniProtKB:  Q8DBF5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DBF5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ARG

Query on ARG



Download:Ideal Coordinates CCD File
I [auth A]ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
SRT

Query on SRT



Download:Ideal Coordinates CCD File
K [auth B]S,R MESO-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-XIXRPRMCSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
J [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.215 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.165α = 90
b = 149.129β = 90
c = 245.089γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-12
    Type: Initial release
  • Version 1.1: 2019-06-12
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description