High-resolution structure of the M14-type cytosolic carboxypeptidase from Burkholderia cenocepacia refined exploiting PDB_REDO strategies

A potential cytosolic metallocarboxypeptidase from Burkholderia cenocepacia has been crystallized and a synchrotron‐radiation microfocus beamline allowed the acquisition of diffraction data to 1.9 Å resolution. The asymmetric unit comprises a tetramer containing over 1500 amino acids, and the high‐t...

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Veröffentlicht in:Acta crystallographica. Section D, Biological crystallography. Biological crystallography., 2014-02, Vol.70 (2), p.279-289
Hauptverfasser: Rimsa, Vadim, Eadsforth, Thomas C., Joosten, Robbie P., Hunter, William N.
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container_title Acta crystallographica. Section D, Biological crystallography.
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creator Rimsa, Vadim
Eadsforth, Thomas C.
Joosten, Robbie P.
Hunter, William N.
description A potential cytosolic metallocarboxypeptidase from Burkholderia cenocepacia has been crystallized and a synchrotron‐radiation microfocus beamline allowed the acquisition of diffraction data to 1.9 Å resolution. The asymmetric unit comprises a tetramer containing over 1500 amino acids, and the high‐throughput automated protocols embedded in PDB_REDO were coupled with model–map inspections in refinement. This approach has highlighted the value of such protocols for efficient analyses. The subunit is constructed from two domains. The N‐terminal domain has previously only been observed in cytosolic carboxypeptidase (CCP) proteins. The C‐terminal domain, which carries the Zn2+‐containing active site, serves to classify this protein as a member of the M14D subfamily of carboxypeptidases. Although eukaryotic CCPs possess deglutamylase activity and are implicated in processing modified tubulin, the function and substrates of the bacterial family members remain unknown. The B. cenocepacia protein did not display deglutamylase activity towards a furylacryloyl glutamate derivative, a potential substrate. Residues previously shown to coordinate the divalent cation and that contribute to peptide‐bond cleavage in related enzymes such as bovine carboxypeptidase are conserved. The location of a conserved basic patch in the active site adjacent to the catalytic Zn2+, where an acetate ion is identified, suggests recognition of the carboxy‐terminus in a similar fashion to other carboxypeptidases. However, there are significant differences that indicate the recognition of substrates with different properties. Of note is the presence of a lysine in the S1′ recognition subsite that suggests specificity towards an acidic substrate.
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Section D, Biological crystallography.</jtitle><addtitle>Acta Crystallographica D</addtitle><date>2014-02</date><risdate>2014</risdate><volume>70</volume><issue>2</issue><spage>279</spage><epage>289</epage><pages>279-289</pages><issn>1399-0047</issn><issn>0907-4449</issn><eissn>1399-0047</eissn><abstract>A potential cytosolic metallocarboxypeptidase from Burkholderia cenocepacia has been crystallized and a synchrotron‐radiation microfocus beamline allowed the acquisition of diffraction data to 1.9 Å resolution. The asymmetric unit comprises a tetramer containing over 1500 amino acids, and the high‐throughput automated protocols embedded in PDB_REDO were coupled with model–map inspections in refinement. This approach has highlighted the value of such protocols for efficient analyses. The subunit is constructed from two domains. The N‐terminal domain has previously only been observed in cytosolic carboxypeptidase (CCP) proteins. 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subjects ACETATES
Amino Acid Sequence
Animals
Bacterial Proteins - chemistry
Bacterial Proteins - genetics
Biocatalysis
Burkholderia cenocepacia - chemistry
Burkholderia cenocepacia - enzymology
carboxypeptidases
Carboxypeptidases - chemistry
Carboxypeptidases - genetics
Catalytic Domain
CATIONS
Cations, Divalent
CATTLE
CLEAVAGE
CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY
Crystallography, X-Ray
CRYSTALS
DIFFRACTION
Kinetics
LYSINE
metalloproteins
METALS
Models, Molecular
Molecular Sequence Data
POTENTIALS
PROCESSING
Protein Multimerization
Protein Structure, Secondary
Protein Structure, Tertiary
Recombinant Proteins - chemistry
Recombinant Proteins - genetics
refinement
Research Papers
RESOLUTION
SPECIFICITY
Substrate Specificity
SUBSTRATES
SYNCHROTRON RADIATION
Synchrotrons
Zinc - chemistry
zinc enzymes
title High-resolution structure of the M14-type cytosolic carboxypeptidase from Burkholderia cenocepacia refined exploiting PDB_REDO strategies
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