5ypd: Difference between revisions
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==Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C105N mutant) in complex with Methionine== | ==Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C105N mutant) in complex with Methionine== | ||
<StructureSection load='5ypd' size='340' side='right' caption='[[5ypd]], [[Resolution|resolution]] 1.62Å' scene=''> | <StructureSection load='5ypd' size='340' side='right'caption='[[5ypd]], [[Resolution|resolution]] 1.62Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5ypd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YPD OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[5ypd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Ra Mycobacterium tuberculosis H37Ra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YPD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YPD FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.62Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5ypd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ypd OCA], [https://pdbe.org/5ypd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ypd RCSB], [https://www.ebi.ac.uk/pdbsum/5ypd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ypd ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/A5U6L5_MYCTA A5U6L5_MYCTA] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Methionine aminopeptidases (MetAPs) are a class of enzymes evolved to cleave initiator methionine in 60-70% of the total cellular proteins in all living cells. Based on their sequence differences, they are classified into Type 1 and Type 2. Type 1 is further divided into Type 1a, 1a', 1b, 1c and 1d. Irrespective of various classifications, all MetAPs reported till date displayed hydrolytic activity against peptides that contain only methionine on the N-terminus. A cysteine at the top of the active site in all the Type 1 structures is reported to be critical for the specificity. Mutation of this cysteine to serine or asparagine leads to loss of specificity. In the present study, we have identified a class of MetAPs in some of the proteobacteria that have an asparagine at this site. Most of the proteobacteria that contain MetAP1n are pathogenic in nature. Biochemical and structural studies on two proteins, one from each of V. coralliilyticus and K. pneumoniae confirm that these enzymes cleave leucine in addition to methionine. Crystallographic and homology modeling studies suggest that relaxed substrate specificity of this new class of enzymes could be due to the increased flexibility in the active site. Since this new class has an asparagine at the critical position that probably contributes for the relaxed substrate specificity and also differentiates them from other Type 1 MetAPs, we classified them as Type 1n. | |||
Discovery of a new class of type 1 methionine aminopeptidases that have relaxed substrate specificity.,Bala SC, Haque N, Pillalamarri V, Reddi R, Kashyap R, Marapaka AK, Addlagatta A Int J Biol Macromol. 2019 May 15;129:523-529. doi:, 10.1016/j.ijbiomac.2019.02.055. Epub 2019 Feb 11. PMID:30763644<ref>PMID:30763644</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 5ypd" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Mycobacterium tuberculosis H37Ra]] | ||
[[Category: | [[Category: Addlagatta A]] | ||
[[Category: | [[Category: Sandeep CB]] | ||
Latest revision as of 11:34, 22 November 2023
Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C105N mutant) in complex with MethionineMycobacterium Tuberculosis Methionine aminopeptidase type 1c (C105N mutant) in complex with Methionine
Structural highlights
FunctionPublication Abstract from PubMedMethionine aminopeptidases (MetAPs) are a class of enzymes evolved to cleave initiator methionine in 60-70% of the total cellular proteins in all living cells. Based on their sequence differences, they are classified into Type 1 and Type 2. Type 1 is further divided into Type 1a, 1a', 1b, 1c and 1d. Irrespective of various classifications, all MetAPs reported till date displayed hydrolytic activity against peptides that contain only methionine on the N-terminus. A cysteine at the top of the active site in all the Type 1 structures is reported to be critical for the specificity. Mutation of this cysteine to serine or asparagine leads to loss of specificity. In the present study, we have identified a class of MetAPs in some of the proteobacteria that have an asparagine at this site. Most of the proteobacteria that contain MetAP1n are pathogenic in nature. Biochemical and structural studies on two proteins, one from each of V. coralliilyticus and K. pneumoniae confirm that these enzymes cleave leucine in addition to methionine. Crystallographic and homology modeling studies suggest that relaxed substrate specificity of this new class of enzymes could be due to the increased flexibility in the active site. Since this new class has an asparagine at the critical position that probably contributes for the relaxed substrate specificity and also differentiates them from other Type 1 MetAPs, we classified them as Type 1n. Discovery of a new class of type 1 methionine aminopeptidases that have relaxed substrate specificity.,Bala SC, Haque N, Pillalamarri V, Reddi R, Kashyap R, Marapaka AK, Addlagatta A Int J Biol Macromol. 2019 May 15;129:523-529. doi:, 10.1016/j.ijbiomac.2019.02.055. Epub 2019 Feb 11. PMID:30763644[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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