| |
Molecular
Biology and Genetics |
| Electronic Journal of Biotechnology ISSN: 0717-3458
|
Vol. 6 No. 1, Issue of April 15, 2003 |
| © 2003 by Universidad Católica de Valparaíso
-- Chile |
Received June 26, 2002 / Accepted March 25, 2003 |
A predicted structure of the cytochrome c oxidase from Burkholderia
pseudomallei Mohd.
Firdaus Mohd. Raih
Centre
for Gene Analysis and Technology
School of BioSciences and Biotechnology
Faculty of Science and Technology
Universiti Kebangsaan Malaysia
43600 UKM Bangi, Malaysia
Tel: +6 03 89267446
Fax: +6 03 89267972
E-mail: mfirr@cgat.ukm.my
Ahmad
Tarmidi Sailan
Centre for Gene Analysis and
Technology
School of BioSciences and Biotechnology
Faculty of Science and Technology
Universiti Kebangsaan Malaysia
43600 UKM Bangi, Malaysia
Tel: +6 03 89267446
Fax: +6 03 89267972
E-mail: tarmidi@medic.ukm.my
Zulkeflie
Zamrod
Centre for Gene Analysis
and Technology
School of BioSciences and Biotechnology
Faculty of Science and Technology
Universiti Kebangsaan Malaysia
43600 UKM Bangi, Malaysia
Tel: +6 03 89267446
Fax: +6 03 89267972
E-mail: zza@pkrisc.cc.ukm.my
Mohd.
Noor Embi
Centre
for Gene Analysis and Technology
School of BioSciences and Biotechnology
Faculty of Science and Technology
Universiti Kebangsaan Malaysia
43600 UKM Bangi, Malaysia
Tel: +6 03 89267446
Fax: +6 03 89267972
E-mail: noormb@pkrisc.cc.ukm.my
Rahmah
Mohamed*
Centre
for Gene Analysis and Technology
School of BioSciences and Biotechnology
Faculty of Science and Technology
Universiti Kebangsaan Malaysia
43600 UKM Bangi, Malaysia
Tel: +6 03 89267446
Fax: +6 03 89267972
E-mail: ram@cgat.ukm.my
http://cgat.ukm.my
* Corresponding author
Financial support: This
work was funded by the Intensification of Research in Priority Areas
(IRPA) grants IRPA 01-02-02-001 and IRPA-TOPDOWN 09-02-02-T001 provided
by the Ministry of Science, Technology and the Environment, Malaysia.
Keywords: Burkholderia
pseudomallei, cytochrome c oxidase, protein structure prediction,
sequence alignments, structure-function extrapolation.
| Acronyms: |
Cox1: B. pseudomallei predicted cytochrome
c oxidase subunit 1 protein;
Bp cox1: B. pseudomallei predicted cytocrome c
oxidase subunit 1 gene;
SU: subunit;
ORF: open reading frame;
BLAST: Basic Local Alignment Search Tool;
TM: transmembrane;
TMH: transmembrane helices;
CVFF: consistent valence force field. |
Cytochrome c
oxidase, the terminal enzyme of the respiratory chains of mitochondria
and aerobic bacteria, catalyzes electron transfer from cytochrome c
to molecular oxygen. The enzyme belongs to the haem-copper-containing
oxidases superfamily. A recombinant plasmid carrying a 2.0 kb insert
from a Burkholderia pseudomallei genomic library was subjected
to automated DNA sequencing utilizing a primer walking strategy.
Analysis of the 2002 bp insert revealed a 1536 bp open reading frame
predicted to encode a putative cytochrome c oxidase. Further
analysis using sequence alignments and tertiary structure analysis tools
demonstrated that the hypothetical B. pseudomallei cytochrome
c oxidase is similar to cytochrome c oxidases from other
organisms such as Thermus thermophilus (36% protein sequence
identity), Paracoccus denitrificans and bovine heart mitochondrial,
the latter two which crystal structures available. The deduced 512 residue
protein sequence includes the six canonical histidine residues involved
in binding the low spin heme B and the binuclear center CuB/hemeA.
The predicted tertiary structure of the hypothetical protein is consistent
with previous models of electron transfer for cytochrome c oxidase.
| 