4x7g: Difference between revisions

Revision as of 21:16, 12 April 2023

CobK precorrin-6A reductase

Structural highlights

4x7g is a 1 chain structure with sequence from Rhodobacter capsulatus SB 1003. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	3Y8, MSE, NAP
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

COBK_RHOCB Catalyzes the reduction of the macrocycle of precorrin-6X into precorrin-6Y.

Publication Abstract from PubMed

CobK catalyzes the essential reduction of the precorrin ring in the cobalamin biosynthetic pathway. The crystal structure of CobK reveals that the enzyme, despite not having the signature sequence, comprises two Rossmann fold domains which bind coenzyme and substrate respectively. The two parallel beta-sheets have swapped their last beta-strands giving a novel sheet topology which is an interesting variation on the Rossmann-fold. The trapped ternary complex with coenzyme and product reveals five conserved basic residues that bind the carboxylates of the tetrapyrrole tightly anchoring the product. A loop, disordered in both the apoenzyme and holoenzyme structures, closes around the product further tightening binding. The structure is consistent with a mechanism involving protonation of C18 and pro-R hydride transfer from NADPH to C19 of precorrin-6A and reveals the interactions responsible for the specificity of CobK. The almost complete burial of the reduced precorrin product suggests a remarkable form of metabolite channeling where the next enzyme in the biosynthetic pathway triggers product release.

Crystal structure of CobK reveals strand-swapping between Rossmann-fold domains and molecular basis of the reduced precorrin product trap.,Gu S, Sushko O, Deery E, Warren MJ, Pickersgill RW Sci Rep. 2015 Nov 30;5:16943. doi: 10.1038/srep16943. PMID:26616290^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Gu S, Sushko O, Deery E, Warren MJ, Pickersgill RW. Crystal structure of CobK reveals strand-swapping between Rossmann-fold domains and molecular basis of the reduced precorrin product trap. Sci Rep. 2015 Nov 30;5:16943. doi: 10.1038/srep16943. PMID:26616290 doi:https://dx.doi.org/10.1038/srep16943

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Gu S, Sushko O, Deery E, Warren MJ, Pickersgill RW. Crystal structure of CobK reveals strand-swapping between Rossmann-fold domains and molecular basis of the reduced precorrin product trap. Sci Rep. 2015 Nov 30;5:16943. doi: 10.1038/srep16943. PMID:26616290 doi:https://dx.doi.org/10.1038/srep16943

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='4x7g' size='340' side='right'caption='[[4x7g]], [[Resolution|resolution]] 1.22&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4x7g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhocb Rhocb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X7G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X7G FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4x7g]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodobacter_capsulatus_SB_1003 Rhodobacter capsulatus SB 1003]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X7G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X7G FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3Y8:3-[(1R,2S,3S,7S,11S,16S,17R,18R,19R)-2,7,12,18-tetrakis(2-hydroxy-2-oxoethyl)-3,13-bis(3-hydroxy-3-oxopropyl)-1,2,5,7,11,17-hexamethyl-17-(3-oxidanyl-3-oxidanylidene-prop-1-enyl)-3,6,8,10,15,16,18,19,21,24-decahydrocorrin-8-yl]propanoic+acid'>3Y8</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3Y8:3-[(1R,2S,3S,7S,11S,16S,17R,18R,19R)-2,7,12,18-tetrakis(2-hydroxy-2-oxoethyl)-3,13-bis(3-hydroxy-3-oxopropyl)-1,2,5,7,11,17-hexamethyl-17-(3-oxidanyl-3-oxidanylidene-prop-1-enyl)-3,6,8,10,15,16,18,19,21,24-decahydrocorrin-8-yl]propanoic+acid'>3Y8</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=4x7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x7g OCA], [https://pdbe.org/4x7g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x7g RCSB], [https://www.ebi.ac.uk/pdbsum/4x7g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x7g ProSAT]</span></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5c4r|5c4r]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cobK, RCAP_rcc02043 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272942 RHOCB])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Precorrin-6A_reductase Precorrin-6A reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.54 1.3.1.54] </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=4x7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x7g OCA], [http://pdbe.org/4x7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x7g RCSB], [http://www.ebi.ac.uk/pdbsum/4x7g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x7g ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/COBK_RHOCB COBK_RHOCB]] Catalyzes the reduction of the macrocycle of precorrin-6X into precorrin-6Y.
+[https://www.uniprot.org/uniprot/COBK_RHOCB COBK_RHOCB] Catalyzes the reduction of the macrocycle of precorrin-6X into precorrin-6Y.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 27: / Line 23: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Precorrin-6A reductase]]
+[[Category: Rhodobacter capsulatus SB 1003]]
-[[Category: Rhocb]]
+[[Category: Deery E]]
-[[Category: Deery, E]]
+[[Category: Gu S]]
-[[Category: Gu, S]]
+[[Category: Pickersgill RW]]
-[[Category: Pickersgill, R W]]
+[[Category: Warren MJ]]
-[[Category: Warren, M J]]
-[[Category: Nadp binding]]
-[[Category: Oxidoreductase]]

4x7g: Difference between revisions

Revision as of 21:16, 12 April 2023

CobK precorrin-6A reductase

Structural highlights

Function

Publication Abstract from PubMed

References

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