3VCR

Crystal structure of a putative Kdpg (2-keto-3-deoxy-6-phosphogluconate) aldolase from Oleispira antarctica


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica.

Kube, M.Chernikova, T.N.Al-Ramahi, Y.Beloqui, A.Lopez-Cortez, N.Guazzaroni, M.E.Heipieper, H.J.Klages, S.Kotsyurbenko, O.R.Langer, I.Nechitaylo, T.Y.Lunsdorf, H.Fernandez, M.Juarez, S.Ciordia, S.Singer, A.Kagan, O.Egorova, O.Alain Petit, P.Stogios, P.Kim, Y.Tchigvintsev, A.Flick, R.Denaro, R.Genovese, M.Albar, J.P.Reva, O.N.Martinez-Gomariz, M.Tran, H.Ferrer, M.Savchenko, A.Yakunin, A.F.Yakimov, M.M.Golyshina, O.V.Reinhardt, R.Golyshin, P.N.

(2013) Nat Commun 4: 2156-2156

  • DOI: 10.1038/ncomms3156
  • Primary Citation of Related Structures:  
    3QVM, 3VCR, 3IRU, 3LMB, 3LNP, 3M16, 3V77, 3I4Q

  • PubMed Abstract: 
  • Ubiquitous bacteria from the genus Oleispira drive oil degradation in the largest environment on Earth, the cold and deep sea. Here we report the genome sequence of Oleispira antarctica and show that compared with Alcanivorax borkumensis--the paradig ...

    Ubiquitous bacteria from the genus Oleispira drive oil degradation in the largest environment on Earth, the cold and deep sea. Here we report the genome sequence of Oleispira antarctica and show that compared with Alcanivorax borkumensis--the paradigm of mesophilic hydrocarbonoclastic bacteria--O. antarctica has a larger genome that has witnessed massive gene-transfer events. We identify an array of alkane monooxygenases, osmoprotectants, siderophores and micronutrient-scavenging pathways. We also show that at low temperatures, the main protein-folding machine Cpn60 functions as a single heptameric barrel that uses larger proteins as substrates compared with the classical double-barrel structure observed at higher temperatures. With 11 protein crystal structures, we further report the largest set of structures from one psychrotolerant organism. The most common structural feature is an increased content of surface-exposed negatively charged residues compared to their mesophilic counterparts. Our findings are relevant in the context of microbial cold-adaptation mechanisms and the development of strategies for oil-spill mitigation in cold environments.


    Organizational Affiliation

    Max-Planck Institute for Molecular Genetics, Berlin-Dahlem D-14195, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
putative Kdpg (2-keto-3-deoxy-6-phosphogluconate) aldolaseAB217Oleispira antarcticaMutation(s): 0 
EC: 4.1.2.14
Find proteins for D2YW47 (Oleispira antarctica)
Explore D2YW47 
Go to UniProtKB:  D2YW47
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PYR
Query on PYR

Download CCD File 
A, B
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.02α = 90
b = 76.02β = 90
c = 241.121γ = 120
Software Package:
Software NamePurpose
StructureStudiodata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-18
    Type: Initial release
  • Version 1.1: 2013-07-24
    Changes: Database references
  • Version 1.2: 2013-08-07
    Changes: Database references