4nv5: Difference between revisions

Revision as of 08:41, 18 January 2023

C50A mutant of Synechococcus VKOR, C2 crystal form (dehydrated)

Structural highlights

4nv5 is a 2 chain structure with sequence from Synechococcus sp. JA-2-3B'a(2-13). Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	U10
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

VKOR_SYNJB Thiol-disulfide oxidoreductase that catalyzes vitamin K-dependent disulfide bond formation in periplasmic target proteins.^[1] ^[2]

Publication Abstract from PubMed

The intramembrane vitamin K epoxide reductase (VKOR) supports blood coagulation in humans and is the target of the anticoagulant warfarin. VKOR and its homologues generate disulphide bonds in organisms ranging from bacteria to humans. Here, to better understand the mechanism of VKOR catalysis, we report two crystal structures of a bacterial VKOR captured in different reaction states. These structures reveal a short helix at the hydrophobic active site of VKOR that alters between wound and unwound conformations. Motions of this 'horizontal helix' promote electron transfer by regulating the positions of two cysteines in an adjacent loop. Winding of the helix separates these 'loop cysteines' to prevent backward electron flow. Despite these motions, hydrophobicity at the active site is maintained to facilitate VKOR catalysis. Biochemical experiments suggest that several warfarin-resistant mutations act by changing the conformation of the horizontal helix. Taken together, these studies provide a comprehensive understanding of VKOR function.

Structures of an intramembrane vitamin K epoxide reductase homolog reveal control mechanisms for electron transfer.,Liu S, Cheng W, Fowle Grider R, Shen G, Li W Nat Commun. 2014 Jan 29;5:3110. doi: 10.1038/ncomms4110. PMID:24477003^[3]

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

References

↑ Li W, Schulman S, Dutton RJ, Boyd D, Beckwith J, Rapoport TA. Structure of a bacterial homologue of vitamin K epoxide reductase. Nature. 2010 Jan 28;463(7280):507-12. PMID:20110994 doi:10.1038/nature08720
↑ Liu S, Cheng W, Fowle Grider R, Shen G, Li W. Structures of an intramembrane vitamin K epoxide reductase homolog reveal control mechanisms for electron transfer. Nat Commun. 2014 Jan 29;5:3110. doi: 10.1038/ncomms4110. PMID:24477003 doi:https://dx.doi.org/10.1038/ncomms4110
↑ Liu S, Cheng W, Fowle Grider R, Shen G, Li W. Structures of an intramembrane vitamin K epoxide reductase homolog reveal control mechanisms for electron transfer. Nat Commun. 2014 Jan 29;5:3110. doi: 10.1038/ncomms4110. PMID:24477003 doi:https://dx.doi.org/10.1038/ncomms4110

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Li W, Schulman S, Dutton RJ, Boyd D, Beckwith J, Rapoport TA. Structure of a bacterial homologue of vitamin K epoxide reductase. Nature. 2010 Jan 28;463(7280):507-12. PMID:20110994 doi:10.1038/nature08720

[2] Liu S, Cheng W, Fowle Grider R, Shen G, Li W. Structures of an intramembrane vitamin K epoxide reductase homolog reveal control mechanisms for electron transfer. Nat Commun. 2014 Jan 29;5:3110. doi: 10.1038/ncomms4110. PMID:24477003 doi:https://dx.doi.org/10.1038/ncomms4110

[3] Liu S, Cheng W, Fowle Grider R, Shen G, Li W. Structures of an intramembrane vitamin K epoxide reductase homolog reveal control mechanisms for electron transfer. Nat Commun. 2014 Jan 29;5:3110. doi: 10.1038/ncomms4110. PMID:24477003 doi:https://dx.doi.org/10.1038/ncomms4110

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==C50A mutant of Synechococcus VKOR, C2 crystal form (dehydrated)==
-<StructureSection load='4nv5' size='340' side='right' caption='[[4nv5]], [[Resolution|resolution]] 2.79&Aring;' scene=''>
+<StructureSection load='4nv5' size='340' side='right'caption='[[4nv5]], [[Resolution|resolution]] 2.79&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4nv5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cyanobacteria_bacterium_yellowstone_b' Cyanobacteria bacterium yellowstone b']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NV5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NV5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4nv5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechococcus_sp._JA-2-3B'a(2-13) Synechococcus sp. JA-2-3B'a(2-13)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NV5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NV5 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=U10:UBIQUINONE-10'>U10</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=U10:UBIQUINONE-10'>U10</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4nv2|4nv2]], [[4nv6|4nv6]], [[3kp9|3kp9]], [[3kp8|3kp8]]</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=4nv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nv5 OCA], [https://pdbe.org/4nv5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nv5 RCSB], [https://www.ebi.ac.uk/pdbsum/4nv5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nv5 ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CYB_2278 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=321332 Cyanobacteria bacterium Yellowstone B'])</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=4nv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nv5 OCA], [http://pdbe.org/4nv5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nv5 RCSB], [http://www.ebi.ac.uk/pdbsum/4nv5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nv5 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/VKOR_SYNJB VKOR_SYNJB] Thiol-disulfide oxidoreductase that catalyzes vitamin K-dependent disulfide bond formation in periplasmic target proteins.<ref>PMID:20110994</ref> <ref>PMID:24477003</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Cyanobacteria bacterium yellowstone b']]
+[[Category: Large Structures]]
-[[Category: Cheng, W]]
+[[Category: Cheng W]]
-[[Category: Grider, R Fowle]]
+[[Category: Fowle Grider R]]
-[[Category: Li, W]]
+[[Category: Li W]]
-[[Category: Liu, S]]
+[[Category: Liu S]]
-[[Category: Shen, G]]
+[[Category: Shen G]]
-[[Category: Four helix bundle]]
-[[Category: Membrane]]
-[[Category: Oxidoreductase]]
-[[Category: Thioredoxin-like protein]]

4nv5: Difference between revisions

Revision as of 08:41, 18 January 2023

C50A mutant of Synechococcus VKOR, C2 crystal form (dehydrated)

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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