4mlv: Difference between revisions
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The | ==Crystal Structure of Bacillus megaterium porphobilinogen deaminase== | ||
<StructureSection load='4mlv' size='340' side='right'caption='[[4mlv]], [[Resolution|resolution]] 1.46Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4mlv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Priestia_megaterium Priestia megaterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MLV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MLV 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]] 1.455Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=29P:3-[(5S)-5-{[3-(2-CARBOXYETHYL)-4-(CARBOXYMETHYL)-5-METHYL-1H-PYRROL-2-YL]METHYL}-4-(CARBOXYMETHYL)-2-OXO-2,5-DIHYDRO-1H-PYRROL-3-YL]PROPANOIC+ACID'>29P</scene>, <scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=DPM:3-[5-{[3-(2-CARBOXYETHYL)-4-(CARBOXYMETHYL)-5-METHYL-1H-PYRROL-2-YL]METHYL}-4-(CARBOXYMETHYL)-1H-PYRROL-3-YL]PROPANOIC+ACID'>DPM</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=4mlv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mlv OCA], [https://pdbe.org/4mlv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mlv RCSB], [https://www.ebi.ac.uk/pdbsum/4mlv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mlv ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q8GCA8_PRIMG Q8GCA8_PRIMG] Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps.[ARBA:ARBA00002869][HAMAP-Rule:MF_00260] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses an early step of the tetrapyrrole-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor, which is covalently linked by a thioether bridge to an invariant cysteine residue (Cys241 in the Bacillus megaterium enzyme). The cofactor is extended during the reaction by the sequential addition of the four substrate molecules, which are released as a linear tetrapyrrole product. Expression in Escherichia coli of a His-tagged form of B. megaterium PBGD has permitted the X-ray analysis of the enzyme from this species at high resolution, showing that the cofactor becomes progressively oxidized to the dipyrromethene and dipyrromethanone forms. In previously solved PBGD structures, the oxidized cofactor is in the dipyromethenone form, in which both pyrrole rings are approximately coplanar. In contrast, the oxidized cofactor in the B. megaterium enzyme appears to be in the dipyrromethanone form, in which the C atom at the bridging alpha-position of the outer pyrrole ring is very clearly in a tetrahedral configuration. It is suggested that the pink colour of the freshly purified protein is owing to the presence of the dipyrromethene form of the cofactor which, in the structure reported here, adopts the same conformation as the fully reduced dipyrromethane form. | |||
Structural evidence for the partially oxidized dipyrromethene and dipyrromethanone forms of the cofactor of porphobilinogen deaminase: structures of the Bacillus megaterium enzyme at near-atomic resolution.,Azim N, Deery E, Warren MJ, Wolfenden BA, Erskine P, Cooper JB, Coker A, Wood SP, Akhtar M Acta Crystallogr D Biol Crystallogr. 2014 Mar;70(Pt 3):744-51. doi:, 10.1107/S139900471303294X. Epub 2014 Feb 15. PMID:24598743<ref>PMID:24598743</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4mlv" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Porphobilinogen Deaminase|Porphobilinogen Deaminase]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Priestia megaterium]] | |||
[[Category: Akhtar M]] | |||
[[Category: Azim N]] | |||
[[Category: Coker A]] | |||
[[Category: Cooper JB]] | |||
[[Category: Deery E]] | |||
[[Category: Erskine P]] | |||
[[Category: Warren MJ]] | |||
[[Category: Wood SP]] | |||
Latest revision as of 19:39, 20 September 2023
Crystal Structure of Bacillus megaterium porphobilinogen deaminaseCrystal Structure of Bacillus megaterium porphobilinogen deaminase
Structural highlights
FunctionQ8GCA8_PRIMG Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps.[ARBA:ARBA00002869][HAMAP-Rule:MF_00260] Publication Abstract from PubMedThe enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses an early step of the tetrapyrrole-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor, which is covalently linked by a thioether bridge to an invariant cysteine residue (Cys241 in the Bacillus megaterium enzyme). The cofactor is extended during the reaction by the sequential addition of the four substrate molecules, which are released as a linear tetrapyrrole product. Expression in Escherichia coli of a His-tagged form of B. megaterium PBGD has permitted the X-ray analysis of the enzyme from this species at high resolution, showing that the cofactor becomes progressively oxidized to the dipyrromethene and dipyrromethanone forms. In previously solved PBGD structures, the oxidized cofactor is in the dipyromethenone form, in which both pyrrole rings are approximately coplanar. In contrast, the oxidized cofactor in the B. megaterium enzyme appears to be in the dipyrromethanone form, in which the C atom at the bridging alpha-position of the outer pyrrole ring is very clearly in a tetrahedral configuration. It is suggested that the pink colour of the freshly purified protein is owing to the presence of the dipyrromethene form of the cofactor which, in the structure reported here, adopts the same conformation as the fully reduced dipyrromethane form. Structural evidence for the partially oxidized dipyrromethene and dipyrromethanone forms of the cofactor of porphobilinogen deaminase: structures of the Bacillus megaterium enzyme at near-atomic resolution.,Azim N, Deery E, Warren MJ, Wolfenden BA, Erskine P, Cooper JB, Coker A, Wood SP, Akhtar M Acta Crystallogr D Biol Crystallogr. 2014 Mar;70(Pt 3):744-51. doi:, 10.1107/S139900471303294X. Epub 2014 Feb 15. PMID:24598743[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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