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

Experimental Data Snapshot

  • Resolution: 1.84 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

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This is version 2.0 of the entry. See complete history


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

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
putative Kdpg (2-keto-3-deoxy-6-phosphogluconate) aldolase
A, B
217Oleispira antarcticaMutation(s): 0 
Find proteins for D2YW47 (Oleispira antarctica)
Explore D2YW47 
Go to UniProtKB:  D2YW47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2YW47
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • 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
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection