3VCR

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

Replaces:  3LAB

Summary for 3VCR

• Entry DOI: 10.2210/pdb3vcr/pdb
• Descriptor: putative Kdpg (2-keto-3-deoxy-6-phosphogluconate) aldolase, PYRUVIC ACID (3 entities in total)
• Functional Keywords: unknown function, aldolase superfamily, class i aldolase, kdpg aldolase domain, alpha/beta protein, tim beta/alpha barrel, tim barrel, structural genomics, psi-2, protein structure initiative, midwest center for structural genomics, mcsg
• Biological source: Oleispira antarctica
• Total number of polymer chains: 2
• Total formula weight: 46076.42

Authors

Stogios, P.J.,Kagan, O.,Di Leo, R.,Yim, V.,Joachimiak, A.,Edwards, A.M.,Savchenko, A.,Midwest Center for Structural Genomics (MCSG) (deposition date: 2012-01-04, release date: 2012-01-18, Last modification date: 2024-11-27)

Primary citation

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.
Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica.
Nat Commun, 4:2156-2156, 2013

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.

PubMed: 23877221
DOI: 10.1038/ncomms3156

Experimental method

X-RAY DIFFRACTION (1.84 Å)