4hf8: Difference between revisions
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The | ==Crystal structure of L-methionine gamma-lyase from Citrobacter freundii with glycine== | ||
<StructureSection load='4hf8' size='340' side='right'caption='[[4hf8]], [[Resolution|resolution]] 2.45Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4hf8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Citrobacter_freundii Citrobacter freundii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HF8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HF8 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]] 2.45Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PLG:N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]'>PLG</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=4hf8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hf8 OCA], [https://pdbe.org/4hf8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hf8 RCSB], [https://www.ebi.ac.uk/pdbsum/4hf8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hf8 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q84AR1_CITFR Q84AR1_CITFR] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The three-dimensional structure of the external aldimine of Citrobacter freundii methionine gamma-lyase with competitive inhibitor glycine has been determined at 2.45 A resolution. It revealed subtle conformational changes providing effective binding of the inhibitor and facilitating labilization of Calpha-protons of the external aldimine. The structure shows that 1, 3-prototropic shift of Calpha-proton to C4'-atom of the cofactor may proceed with participation of active site Lys210 residue whose location is favorable for performing this transformation by a concerted mechanism. The observed stereoselectivity of isotopic exchange of enantiotopic Calpha-protons of glycine may be explained on the basis of external aldimine structure. The exchange of Calpha-pro-(R)-proton of the external aldimine might proceed in the course of the concerted transfer of the proton from Calpha-atom of glycine to C4'-atom of the cofactor. The exchange of Calpha-pro-(S)-proton may be performed with participation of Tyr113 residue which should be present in its basic form. The isotopic exchange of beta-protons, which is observed for amino acids bearing longer side groups, may be effected by two catalytic groups: Lys210 in its basic form, and Tyr113 acting as a general acid. | |||
Crystal structure of the external aldimine of Citrobacter freundii methionine gamma-lyase with glycine provides insight in mechanisms of two stages of physiological reaction and isotope exchange of alpha- and beta-protons of competitive inhibitors.,Revtovich SV, Faleev NG, Morozova EA, Anufrieva NV, Nikulin AD, Demidkina TV Biochimie. 2014 Jun;101:161-7. doi: 10.1016/j.biochi.2014.01.007. Epub 2014 Jan, 24. PMID:24463191<ref>PMID:24463191</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4hf8" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Methionine gamma-lyase 3D structures|Methionine gamma-lyase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Citrobacter freundii]] | |||
[[Category: Large Structures]] | |||
[[Category: Anufrieva NV]] | |||
[[Category: Demidkina TV]] | |||
[[Category: Morozova EA]] | |||
[[Category: Nikulin AD]] | |||
[[Category: Revtovich SV]] | |||
Latest revision as of 17:07, 8 November 2023
Crystal structure of L-methionine gamma-lyase from Citrobacter freundii with glycineCrystal structure of L-methionine gamma-lyase from Citrobacter freundii with glycine
Structural highlights
FunctionPublication Abstract from PubMedThe three-dimensional structure of the external aldimine of Citrobacter freundii methionine gamma-lyase with competitive inhibitor glycine has been determined at 2.45 A resolution. It revealed subtle conformational changes providing effective binding of the inhibitor and facilitating labilization of Calpha-protons of the external aldimine. The structure shows that 1, 3-prototropic shift of Calpha-proton to C4'-atom of the cofactor may proceed with participation of active site Lys210 residue whose location is favorable for performing this transformation by a concerted mechanism. The observed stereoselectivity of isotopic exchange of enantiotopic Calpha-protons of glycine may be explained on the basis of external aldimine structure. The exchange of Calpha-pro-(R)-proton of the external aldimine might proceed in the course of the concerted transfer of the proton from Calpha-atom of glycine to C4'-atom of the cofactor. The exchange of Calpha-pro-(S)-proton may be performed with participation of Tyr113 residue which should be present in its basic form. The isotopic exchange of beta-protons, which is observed for amino acids bearing longer side groups, may be effected by two catalytic groups: Lys210 in its basic form, and Tyr113 acting as a general acid. Crystal structure of the external aldimine of Citrobacter freundii methionine gamma-lyase with glycine provides insight in mechanisms of two stages of physiological reaction and isotope exchange of alpha- and beta-protons of competitive inhibitors.,Revtovich SV, Faleev NG, Morozova EA, Anufrieva NV, Nikulin AD, Demidkina TV Biochimie. 2014 Jun;101:161-7. doi: 10.1016/j.biochi.2014.01.007. Epub 2014 Jan, 24. PMID:24463191[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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