6oad
From Proteopedia
(Difference between revisions)
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==2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B from Escherichia coli str. K-12 substr. MG1655.== | ==2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B from Escherichia coli str. K-12 substr. MG1655.== | ||
| - | <StructureSection load='6oad' size='340' side='right'caption='[[6oad]]' scene=''> | + | <StructureSection load='6oad' size='340' side='right'caption='[[6oad]], [[Resolution|resolution]] 2.05Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OAD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OAD FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6oad]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._MG1655 Escherichia coli str. K-12 substr. MG1655]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OAD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OAD FirstGlance]. <br> |
| - | </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=6oad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oad OCA], [https://pdbe.org/6oad PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6oad RCSB], [https://www.ebi.ac.uk/pdbsum/6oad PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6oad ProSAT]</span></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]] 2.05Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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'>[https://proteopedia.org/fgij/fg.htm?mol=6oad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oad OCA], [https://pdbe.org/6oad PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6oad RCSB], [https://www.ebi.ac.uk/pdbsum/6oad PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6oad ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/PEPB_ECOLI PEPB_ECOLI] Probably plays an important role in intracellular peptide degradation (PubMed:20067529).[HAMAP-Rule:MF_00504]<ref>PMID:20067529</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Protein degradation by aminopeptidases is involved in bacterial responses to stress. Escherichia coli produces two metal-dependent M17 family leucine aminopeptidases (LAPs), aminopeptidase A (PepA) and aminopeptidase B (PepB). Several structures have been solved for PepA as well as other bacterial M17 peptidases. Herein, we report the first structures of a PepB M17 peptidase. The E. coli PepB protein structure was determined at a resolution of 2.05 and 2.6 A. One structure has both Zn(2+) and Mn(2+) , while the second structure has two Zn(2+) ions bound to the active site. A 2.75 A apo structure is also reported for PepB from Yersinia pestis. Both proteins form homohexamers, similar to the overall arrangement of PepA and other M17 peptidases. However, the divergent N-terminal domain in PepB is much larger resulting in a tertiary structure that is more expanded. Modeling of a dipeptide substrate into the C-terminal LAP domain reveals contacts that account for PepB to uniquely cleave after aspartate. | ||
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| + | Comparison of metal-bound and unbound structures of aminopeptidase B proteins from Escherichia coli and Yersinia pestis.,Minasov G, Lam MR, Rosas-Lemus M, Slawek J, Woinska M, Shabalin IG, Shuvalova L, Palsson BO, Godzik A, Minor W, Satchell KJF Protein Sci. 2020 Jul;29(7):1618-1628. doi: 10.1002/pro.3876. Epub 2020 May 8. PMID:32306515<ref>PMID:32306515</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6oad" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
*[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]] | *[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Escherichia coli str. K-12 substr. MG1655]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Grimshaw S]] | [[Category: Grimshaw S]] | ||
Current revision
2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B from Escherichia coli str. K-12 substr. MG1655.
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