4gvq: Difference between revisions
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==X-ray structure of the Archaeoglobus fulgidus methenyl-tetrahydromethanopterin cyclohydrolase in complex with tetrahydromethanpterin== | |||
<StructureSection load='4gvq' size='340' side='right' caption='[[4gvq]], [[Resolution|resolution]] 1.30Å' scene=''> | |||
{{ | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4gvq]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfu Arcfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GVQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GVQ FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=N4M:1-[4-({(1R)-1-[(6S,7S)-2-AMINO-7-METHYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]ETHYL}AMINO)PHENYL]-1-DEOXY-5-O-{5-O-[(R)-{[(1R)-1,3-DICARBOXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]-ALPHA-D-RIBOFURANOSYL}-D-XYLITOL'>N4M</scene></td></tr> | |||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4gvr|4gvr]], [[4gvs|4gvs]]</td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AF_1935, mch ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224325 ARCFU])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methenyltetrahydromethanopterin_cyclohydrolase Methenyltetrahydromethanopterin cyclohydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.27 3.5.4.27] </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=4gvq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gvq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gvq RCSB], [http://www.ebi.ac.uk/pdbsum/4gvq PDBsum]</span></td></tr> | |||
</table> | |||
== Function == | |||
[[http://www.uniprot.org/uniprot/MCH_ARCFU MCH_ARCFU]] Catalyzes the hydrolysis of methenyl-H(4)MPT(+) to 5-formyl-H(4)MPT. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Methenyltetrahydromethanopterin (methenyl-H(4)MPT(+)) cyclohydrolase (Mch) catalyzes the interconversion of methenyl-H(4)MPT(+) and formyl-H(4)MPT in the one-carbon energy metabolism of methanogenic, methanotrophic, and sulfate-reducing archaea and of methylotrophic bacteria. To understand the catalytic mechanism of this reaction, we kinetically characterized site-specific variants of Mch from Archaeoglobus fulgidus (aMch) and determined the X-ray structures of the substrate-free aMch(E186Q), the aMch:H(4)MPT complex, and the aMch(E186Q):formyl-H(4)MPT complex. (Formyl-)H(4)MPT is embedded inside a largely preformed, interdomain pocket of the homotrimeric enzyme with the pterin and benzyl rings being oriented nearly perpendicular to each other. The active site is primarily built up by the segment 93:95, Arg183 and Glu186 that either interact with the catalytic water attacking methenyl-H(4)MPT(+) or with the formyl oxygen of formyl-H(4)MPT. The catalytic function of the strictly conserved Arg183 and Glu186 was substantiated by the low enzymatic activities of the E186A, E186D, E186N, E186Q, R183A, R183Q, R183E, R183K, and R183E-E186Q variants. Glu186 most likely acts as a general base. Arg183 decisively influences the pK(a) value of Glu186 and the proposed catalytic water mainly by its positive charge. In addition, Glu186 appears to be also responsible for product specificity by donating a proton to the directly neighbored N(10) tertiary amine of H(4)MPT. Thus, N(10) becomes a better leaving group than N(5) which implies the generation of N(5)-formyl-H(4)MPT. For comparison, methenyltetrahydrofolate (H(4)F) cyclohydrolase produces N(10)-formyl-H(4)F in an analogous reaction. An enzymatic mechanism of Mch is postulated and compared with that of other cyclohydrolases. | |||
Structure and catalytic mechanism of N(5),N(10)-methenyl-tetrahydromethanopterin cyclohydrolase.,Upadhyay V, Demmer U, Warkentin E, Moll J, Shima S, Ermler U Biochemistry. 2012 Oct 23;51(42):8435-43. doi: 10.1021/bi300777k. Epub 2012 Oct, 8. PMID:23013430<ref>PMID:23013430</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
== | ==See Also== | ||
*[[Cyclohydrolase|Cyclohydrolase]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Arcfu]] | [[Category: Arcfu]] | ||
[[Category: Methenyltetrahydromethanopterin cyclohydrolase]] | [[Category: Methenyltetrahydromethanopterin cyclohydrolase]] | ||
[[Category: Demmer, U | [[Category: Demmer, U]] | ||
[[Category: Ermler, U | [[Category: Ermler, U]] | ||
[[Category: Moll, J | [[Category: Moll, J]] | ||
[[Category: Shima, S | [[Category: Shima, S]] | ||
[[Category: Upadhyay, V | [[Category: Upadhyay, V]] | ||
[[Category: Warkentin, E | [[Category: Warkentin, E]] | ||
[[Category: Hydrolase]] | [[Category: Hydrolase]] | ||
[[Category: Tetrahydromethanopterin]] | [[Category: Tetrahydromethanopterin]] | ||
Revision as of 04:08, 25 December 2014
X-ray structure of the Archaeoglobus fulgidus methenyl-tetrahydromethanopterin cyclohydrolase in complex with tetrahydromethanpterinX-ray structure of the Archaeoglobus fulgidus methenyl-tetrahydromethanopterin cyclohydrolase in complex with tetrahydromethanpterin
Structural highlights
Function[MCH_ARCFU] Catalyzes the hydrolysis of methenyl-H(4)MPT(+) to 5-formyl-H(4)MPT. Publication Abstract from PubMedMethenyltetrahydromethanopterin (methenyl-H(4)MPT(+)) cyclohydrolase (Mch) catalyzes the interconversion of methenyl-H(4)MPT(+) and formyl-H(4)MPT in the one-carbon energy metabolism of methanogenic, methanotrophic, and sulfate-reducing archaea and of methylotrophic bacteria. To understand the catalytic mechanism of this reaction, we kinetically characterized site-specific variants of Mch from Archaeoglobus fulgidus (aMch) and determined the X-ray structures of the substrate-free aMch(E186Q), the aMch:H(4)MPT complex, and the aMch(E186Q):formyl-H(4)MPT complex. (Formyl-)H(4)MPT is embedded inside a largely preformed, interdomain pocket of the homotrimeric enzyme with the pterin and benzyl rings being oriented nearly perpendicular to each other. The active site is primarily built up by the segment 93:95, Arg183 and Glu186 that either interact with the catalytic water attacking methenyl-H(4)MPT(+) or with the formyl oxygen of formyl-H(4)MPT. The catalytic function of the strictly conserved Arg183 and Glu186 was substantiated by the low enzymatic activities of the E186A, E186D, E186N, E186Q, R183A, R183Q, R183E, R183K, and R183E-E186Q variants. Glu186 most likely acts as a general base. Arg183 decisively influences the pK(a) value of Glu186 and the proposed catalytic water mainly by its positive charge. In addition, Glu186 appears to be also responsible for product specificity by donating a proton to the directly neighbored N(10) tertiary amine of H(4)MPT. Thus, N(10) becomes a better leaving group than N(5) which implies the generation of N(5)-formyl-H(4)MPT. For comparison, methenyltetrahydrofolate (H(4)F) cyclohydrolase produces N(10)-formyl-H(4)F in an analogous reaction. An enzymatic mechanism of Mch is postulated and compared with that of other cyclohydrolases. Structure and catalytic mechanism of N(5),N(10)-methenyl-tetrahydromethanopterin cyclohydrolase.,Upadhyay V, Demmer U, Warkentin E, Moll J, Shima S, Ermler U Biochemistry. 2012 Oct 23;51(42):8435-43. doi: 10.1021/bi300777k. Epub 2012 Oct, 8. PMID:23013430[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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