Primary Citation PubMed: 24056934
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Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine.
(2014) MBio 5
PubMed: 24520058 | PubMedCentral: PMC3950512 | DOI: 10.1128/mBio.00933-13
The PDB template used for the two HpbD enzymes is 2PMQ and for pd HpbR is 3HHG .
A monomer from a related proline betaine racemase (J. B. Bonanno, M. Rutter, K. T. Bain, C. Lau, V. Sridhar, D. Smith, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo, New York SGX Research Center for Structural Genomics [NYSGXRC]; PDB 2PMQ) was used as a search model in molecular replacement.
Publication Year: 2014
Discovery of new enzymes and metabolic pathways by using structure and genome context.
(2013) Nature 502
PubMed: 24056934 | PubMedCentral: PMC3966649 | DOI: 10.1038/nature12576
Figure 2 shows the genome neighborhoods of the gene encoding 2PMQ [ hpb D; h ydroxy p roline b etaine from its functional characterization ( vide infra )] plus a putative Paracoccus denitrificans orth... logue.
For docking, 2PMQ, the 1.72 Å X-ray apo structure of HpbD, was used.
The unliganded structure used in docking (PDB 2PMQ) and the later determined liganded structure (PDB 4H2H) are shown in magenta and cyan, respectively.
b. In Vitro Activity Measurements Cloning, Expression, and Purification of the 2PMQ (HpbD) The protein sample was provided by the NYSGXRC structural genomics center (PSI-2; U54GM074945).
Cloning, Expression, and Purification of the 2PMQ Orthologue (HpbD) from P. denitrificans The protein sample was provided by the NYSGXRC structural genomics center.
The unliganded structure (APO) was determined by selenomethionine SAD phasing by the NYSGXRC in 2007 from a C- terminally His-Tagged protein (2PMQ, Supplemental Table S4 ), with a dimer per asymmetric unit.
The results of library docking to the experimental apo structure of HpbD (2PMQ) and to homology models of HpbJ and HpbB1 allowed prediction that HpbD utilizes Hyp-B or Pro-B as substrate in a 1,1-proton transfer reaction.
In summary, we used homology modeling and metabolite docking to several proteins encoded by a gene cluster to guide in vitro assignment of the novel Hyp-B 2-epimerase activity to 2PMQ, a structure determined by the Protein Structure Initiative.
We report that structure-guided approaches for predicting the substrate specificities of several enzymes encoded by a bacterial gene cluster allowed i) the correct prediction of the in vitro activity of a structurally characterized enzyme of unknown function (PDB 2PMQ), 2-epimerization of t rans -4- hy droxy-L- p roline b etaine (tHyp-B) and c is -4- hy droxy-D- p roline b etaine (cHyp-B), and ii) the correct identification of the catabolic pathway in which Hyp-B 2-epimerase participates.
Data deposition The atomic coordinates and structure factors for APO Hyp-B 2-epimerase (HpbD; PDBID:2PMQ) and tHyp-B-liganded HpbD (PDBID:4H2H) have been deposited in the Protein Data Bank, www.pdb.org .
The New York SGX Research Consortium determined its structure (PDB 2PMQ) because it shared <30% sequence identity with structurally characterized enolase superfamily members.
Publication Year: 2013
PubMed ID is not available.
Published in 2014
This work led to the correct prediction of the in vitro activity of a structurally characterized enzyme of unknown function (PDB 2PMQ), and also to the correct identification of the catabolic pathway ... n which Hyp-B 2-epimerase participates.
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