View source for 6koy


==Crystal structure of two domain M1 Zinc metallopeptidase E323A mutant bound to L-tryptophan amino acid==
<StructureSection load='6koy' size='340' side='right'caption='[[6koy]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6koy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KOY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KOY 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]] 2.35&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</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=6koy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6koy OCA], [https://pdbe.org/6koy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6koy RCSB], [https://www.ebi.ac.uk/pdbsum/6koy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6koy ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q9RVZ5_DEIRA Q9RVZ5_DEIRA] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
M1 metallopeptidases regulate many important biological processes such as angiogenesis, tumour growth, hormone regulation, and immune cell development. Knowledge of substrate specificity mechanism in this family is valuable. An M1 peptidase from Deinococcus radiodurans (M1dr) with preference for bulky hydrophobic residues at N-terminus of peptide substrates was recently reported. In contrast to Escherichia coli aminopeptidase N, a previously characterized M1 peptidase, M1dr exhibits reduced activity towards peptides with N-terminal Arg or Ala residue. In order to illuminate structural basis of substrate specificity, we report several crystal structures of M1dr with different amino acids bound to the active site. Structural analysis indicated that the enzyme makes subtle adjustments to multiple residues leading to significant volume change of the active site cavity to accommodate residues of varying sizes (Leu to Trp). This study further reveals that the low preference for Arg at N-terminus of peptide substrate arises from a non-productive conformation in which many of the Arg molecules bind where they block the proton donor essential for the peptidase reaction. Hence, this study illuminates the substrate-binding mechanism and also reveals the structural basis for the substrate specificity of M1dr enzyme.

Structural basis for the unusual substrate specificity of unique two-domain M1 metallopeptidase.,Agrawal R, Goyal VD, Singh R, Kumar A, Jamdar SN, Kumar A, Makde RD Int J Biol Macromol. 2020 Jan 7;147:304-313. doi: 10.1016/j.ijbiomac.2019.12.239. PMID:31923495<ref>PMID:31923495</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6koy" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Deinococcus radiodurans R1]]
[[Category: Large Structures]]
[[Category: Agrawal R]]
[[Category: Kumar A]]
[[Category: Makde RD]]