5wvu

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Crystal structure of carboxypeptidase from Thermus thermophilus

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Categories: Large Structures | Thermus thermophilus HB8 | Nagata K | Okai M | Tanokura M

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 ==Crystal structure of carboxypeptidase from Thermus thermophilus==
-<StructureSection load='5wvu' size='340' side='right' caption='[[5wvu]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+<StructureSection load='5wvu' size='340' side='right'caption='[[5wvu]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5wvu]] is a 3 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1wgz 1wgz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WVU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WVU FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5wvu]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1wgz 1wgz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WVU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WVU FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carboxypeptidase_Taq Carboxypeptidase Taq], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.17.19 3.4.17.19] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5wvu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wvu OCA], [http://pdbe.org/5wvu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wvu RCSB], [http://www.ebi.ac.uk/pdbsum/5wvu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wvu ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5wvu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wvu OCA], [https://pdbe.org/5wvu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wvu RCSB], [https://www.ebi.ac.uk/pdbsum/5wvu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wvu ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CBP1_THET8 CBP1_THET8]] Broad specificity carboxypetidase that releases amino acids sequentially from the C-terminus, including neutral, aromatic, polar and basic residues, but not Pro. Has lower activity with substrates ending with Gly or Glu.<ref>PMID:19544567</ref>
+[https://www.uniprot.org/uniprot/CBP1_THET8 CBP1_THET8] Broad specificity carboxypetidase that releases amino acids sequentially from the C-terminus, including neutral, aromatic, polar and basic residues, but not Pro. Has lower activity with substrates ending with Gly or Glu.<ref>PMID:19544567</ref>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Carboxypeptidase cleaves the C-terminal amino acid residue from proteins and peptides. Here, we report the functional and structural characterizations of carboxypeptidase belonging to the M32 family from the thermophilic bacterium Thermus thermophilus HB8 (TthCP). TthCP exhibits a relatively broad specificity for both hydrophilic (neutral and basic) and hydrophobic (aliphatic and aromatic) residues at the C-terminus and shows optimal activity in the temperature range of 75-80 degrees C and in the pH range of 6.8-7.2. Enzyme activity was significantly enhanced by cobalt or cadmium and was moderately inhibited by Tris at 25 degrees C. We also determined the crystal structure of TthCP at 2.6 A resolution. Two dimer types of TthCP are present in the crystal. One type consists of two subunits in different states, open and closed, with a Calpha RMSD value of 2.2 A; the other type consists of two subunits in the same open state. This structure enables us to compare the open and closed states of an M32 carboxypeptidase. The TthCP subunit can be divided into two domains, L and S, which are separated by a substrate-binding groove. The L and S domains in the open state are almost identical to those in the closed state, with Calpha RMSD values of 0.84 and 0.53 A, respectively, suggesting that the transition between the open and closed states proceeds with a large hinge-bending motion. The superimposition between the closed states of TthCP and BsuCP, another M32 family member, revealed that most putative substrate-binding residues in the grooves are oriented in the same direction.
-Insight into the transition between the open and closed conformations of Thermus thermophilus carboxypeptidase.,Okai M, Yamamura A, Hayakawa K, Tsutsui S, Miyazono KI, Lee WC, Nagata K, Inoue Y, Tanokura M Biochem Biophys Res Commun. 2017 Mar 18;484(4):787-793. doi:, 10.1016/j.bbrc.2017.01.167. Epub 2017 Feb 2. PMID:28161633<ref>PMID:28161633</ref>
+==See Also==
+*[[Carboxypeptidase 3D structures|Carboxypeptidase 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5wvu" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Carboxypeptidase Taq]]
+[[Category: Large Structures]]
-[[Category: Nagata, K]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: Okai, M]]
+[[Category: Nagata K]]
-[[Category: Structural genomic]]
+[[Category: Okai M]]
-[[Category: Tanokura, M]]
+[[Category: Tanokura M]]
-[[Category: Carboxypeptidase]]
-[[Category: Hydrolase]]
-[[Category: Rsgi]]

5wvu

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Crystal structure of carboxypeptidase from Thermus thermophilus

Structural highlights

Function

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References

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