3be7: Difference between revisions
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==Crystal structure of Zn-dependent arginine carboxypeptidase== | |||
<StructureSection load='3be7' size='340' side='right'caption='[[3be7]], [[Resolution|resolution]] 2.30Å' scene=''> | |||
| | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3be7]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Unidentified Unidentified]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BE7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BE7 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=3be7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3be7 OCA], [https://pdbe.org/3be7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3be7 RCSB], [https://www.ebi.ac.uk/pdbsum/3be7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3be7 ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/3be7 TOPSAN]</span></td></tr> | |||
</table> | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/be/3be7_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3be7 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The substrate profiles for two proteins from Caulobacter crescentus CB15 (Cc2672 and Cc3125) and one protein (Sgx9359b) derived from a DNA sequence ( gi|44368820 ) isolated from the Sargasso Sea were determined using combinatorial libraries of dipeptides and N-acyl derivatives of amino acids. These proteins are members of the amidohydrolase superfamily and are currently misannotated in NCBI as catalyzing the hydrolysis of l-Xaa-l-Pro dipeptides. Cc2672 was shown to catalyze the hydrolysis of l-Xaa-l-Arg/Lys dipeptides and the N-acetyl and N-formyl derivatives of lysine and arginine. This enzyme will also hydrolyze longer peptides that terminate in either lysine or arginine. The N-methyl phosphonate derivative of l-lysine was a potent competitive inhibitor of Cc2672 with a K(i) value of 120 nM. Cc3125 was shown to catalyze the hydrolysis of l-Xaa-l-Arg/Lys dipeptides but will not hydrolyze tripeptides or the N-formyl and N-acetyl derivatives of lysine or arginine. The substrate profile for Sgx9359b is similar to that of Cc2672 except that compounds with a C-terminal lysine are not recognized as substrates. The X-ray structure of Sgx9359b was determined to a resolution of 2.3 A. The protein folds as a (beta/alpha)(8)-barrel and self-associates to form a homooctamer. The active site is composed of a binuclear metal center similar to that found in phosphotriesterase and dihydroorotase. In one crystal form, arginine was bound adventitiously to the eight active sites within the octamer. The orientation of the arginine in the active site identified the structural determinants for recognition of the alpha-carboxylate and the positively charged side chains of arginine-containing substrates. This information was used to identify 18 other bacterial sequences that possess identical or similar substrate profiles. | |||
Functional identification of incorrectly annotated prolidases from the amidohydrolase superfamily of enzymes.,Xiang DF, Patskovsky Y, Xu C, Meyer AJ, Sauder JM, Burley SK, Almo SC, Raushel FM Biochemistry. 2009 May 5;48(17):3730-42. PMID:19281183<ref>PMID:19281183</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3be7" style="background-color:#fffaf0;"></div> | |||
== | ==See Also== | ||
*[[Carboxypeptidase 3D structures|Carboxypeptidase 3D structures]] | |||
[[Category: | == References == | ||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Unidentified]] | [[Category: Unidentified]] | ||
[[Category: Almo | [[Category: Almo SC]] | ||
[[Category: Bain | [[Category: Bain K]] | ||
[[Category: Burley | [[Category: Burley SK]] | ||
[[Category: Freeman | [[Category: Freeman J]] | ||
[[Category: Iizuka | [[Category: Iizuka M]] | ||
[[Category: Meyer | [[Category: Meyer AJ]] | ||
[[Category: Patskovsky Y]] | |||
[[Category: Patskovsky | [[Category: Ramagopal UA]] | ||
[[Category: Ramagopal | [[Category: Raushel F]] | ||
[[Category: Raushel | [[Category: Rodgers L]] | ||
[[Category: Rodgers | [[Category: Sauder JM]] | ||
[[Category: Sauder | [[Category: Toro R]] | ||
[[Category: Toro | |||
Latest revision as of 15:07, 30 August 2023
Crystal structure of Zn-dependent arginine carboxypeptidaseCrystal structure of Zn-dependent arginine carboxypeptidase
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe substrate profiles for two proteins from Caulobacter crescentus CB15 (Cc2672 and Cc3125) and one protein (Sgx9359b) derived from a DNA sequence ( gi|44368820 ) isolated from the Sargasso Sea were determined using combinatorial libraries of dipeptides and N-acyl derivatives of amino acids. These proteins are members of the amidohydrolase superfamily and are currently misannotated in NCBI as catalyzing the hydrolysis of l-Xaa-l-Pro dipeptides. Cc2672 was shown to catalyze the hydrolysis of l-Xaa-l-Arg/Lys dipeptides and the N-acetyl and N-formyl derivatives of lysine and arginine. This enzyme will also hydrolyze longer peptides that terminate in either lysine or arginine. The N-methyl phosphonate derivative of l-lysine was a potent competitive inhibitor of Cc2672 with a K(i) value of 120 nM. Cc3125 was shown to catalyze the hydrolysis of l-Xaa-l-Arg/Lys dipeptides but will not hydrolyze tripeptides or the N-formyl and N-acetyl derivatives of lysine or arginine. The substrate profile for Sgx9359b is similar to that of Cc2672 except that compounds with a C-terminal lysine are not recognized as substrates. The X-ray structure of Sgx9359b was determined to a resolution of 2.3 A. The protein folds as a (beta/alpha)(8)-barrel and self-associates to form a homooctamer. The active site is composed of a binuclear metal center similar to that found in phosphotriesterase and dihydroorotase. In one crystal form, arginine was bound adventitiously to the eight active sites within the octamer. The orientation of the arginine in the active site identified the structural determinants for recognition of the alpha-carboxylate and the positively charged side chains of arginine-containing substrates. This information was used to identify 18 other bacterial sequences that possess identical or similar substrate profiles. Functional identification of incorrectly annotated prolidases from the amidohydrolase superfamily of enzymes.,Xiang DF, Patskovsky Y, Xu C, Meyer AJ, Sauder JM, Burley SK, Almo SC, Raushel FM Biochemistry. 2009 May 5;48(17):3730-42. PMID:19281183[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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