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| | ==Crystal structure of Xaa-Pro aminopeptidase from Escherichia coli K12== | | ==Crystal structure of Xaa-Pro aminopeptidase from Escherichia coli K12== |
| - | <StructureSection load='5cnx' size='340' side='right' caption='[[5cnx]], [[Resolution|resolution]] 2.60Å' scene=''> | + | <StructureSection load='5cnx' size='340' side='right'caption='[[5cnx]], [[Resolution|resolution]] 2.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5cnx]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CNX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CNX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5cnx]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CNX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CNX FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ypdF, b2385, JW2382 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=5cnx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cnx OCA], [https://pdbe.org/5cnx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cnx RCSB], [https://www.ebi.ac.uk/pdbsum/5cnx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cnx ProSAT]</span></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=5cnx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cnx OCA], [http://pdbe.org/5cnx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cnx RCSB], [http://www.ebi.ac.uk/pdbsum/5cnx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5cnx ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/YPDF_ECOLI YPDF_ECOLI]] Hydrolyzes the N-terminal methionine when the next amino acid is alanine, proline or serine. The substrate preference for methionyl aminopeptidase activity is Pro > Ala > Ser. Also able to hydrolyze the Xaa-Pro peptide bond when the first amino acid is alanine, asparagine or methionine.<ref>PMID:15901689</ref> | + | [https://www.uniprot.org/uniprot/YPDF_ECOLI YPDF_ECOLI] Hydrolyzes the N-terminal methionine when the next amino acid is alanine, proline or serine. The substrate preference for methionyl aminopeptidase activity is Pro > Ala > Ser. Also able to hydrolyze the Xaa-Pro peptide bond when the first amino acid is alanine, asparagine or methionine.<ref>PMID:15901689</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[Aminopeptidase|Aminopeptidase]] | + | *[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecoli]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Are, V]] | + | [[Category: Large Structures]] |
| - | [[Category: Ghosh, B]] | + | [[Category: Are V]] |
| - | [[Category: Jamdar, S]] | + | [[Category: Ghosh B]] |
| - | [[Category: Kumar, A]] | + | [[Category: Jamdar S]] |
| - | [[Category: Makde, R D]] | + | [[Category: Kumar A]] |
| - | [[Category: Hydrolase]]
| + | [[Category: Makde RD]] |
| - | [[Category: Pepq]]
| + | |
| - | [[Category: Prolidase]]
| + | |
| - | [[Category: Xaa-pro aminopeptidase]]
| + | |
| Structural highlights
Function
YPDF_ECOLI Hydrolyzes the N-terminal methionine when the next amino acid is alanine, proline or serine. The substrate preference for methionyl aminopeptidase activity is Pro > Ala > Ser. Also able to hydrolyze the Xaa-Pro peptide bond when the first amino acid is alanine, asparagine or methionine.[1]
Publication Abstract from PubMed
M24B peptidases cleaving Xaa-Pro bond in dipeptides are prolidases whereas those cleaving this bond in longer peptides are aminopeptidases-P. Bacteria have small aminopeptidases-P (36-39 kDa), which are diverged from canonical aminopeptidase-P of Escherichia coli (50 kDa). Structure-function studies of small aminopeptidases-P are lacking. We report crystal structures of small aminopeptidases-P from E. coli and Deinococcus radiodurans, and report substrate-specificities of these proteins and their ortholog from Mycobacterium tuberculosis. These are aminopeptidases-P, structurally close to small prolidases except for absence of dipeptide-selectivity loop. We noticed absence of this loop and conserved arginine in canonical archaeal prolidase (Maher et al., Biochemistry. 43, 2004, 2771-2783) and questioned its classification. Our enzymatic assays show that this enzyme is an aminopeptidase-P. Further, our mutagenesis studies illuminate importance of DXRY sequence motif in bacterial small aminopeptidases-P and suggest common evolutionary origin with human XPNPEP1/XPNPEP2. Our analyses reveal sequence/structural features distinguishing small aminopeptidases-P from other M24B peptidases.
Structures and activities of widely conserved small prokaryotic aminopeptidases-P clarify classification of M24B peptidases.,Are VN, Kumar A, Goyal VD, Gotad SS, Ghosh B, Gadre R, Jamdar SN, Makde RD Proteins. 2018 Dec 11. doi: 10.1002/prot.25641. PMID:30536999[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Zheng Y, Roberts RJ, Kasif S, Guan C. Characterization of two new aminopeptidases in Escherichia coli. J Bacteriol. 2005 Jun;187(11):3671-7. PMID:15901689 doi:http://dx.doi.org/187/11/3671
- ↑ Are VN, Kumar A, Goyal VD, Gotad SS, Ghosh B, Gadre R, Jamdar SN, Makde RD. Structures and activities of widely conserved small prokaryotic aminopeptidases-P clarify classification of M24B peptidases. Proteins. 2018 Dec 11. doi: 10.1002/prot.25641. PMID:30536999 doi:http://dx.doi.org/10.1002/prot.25641
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