3kp8

From Proteopedia

(Difference between revisions)

Current revision

The thioredoxin-like domain of a VKOR homolog from Synechococcus sp.

Structural highlights

3kp8 is a 1 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.
Method:	X-ray diffraction, Resolution 1.66Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Vitamin K epoxide reductase (VKOR) generates vitamin K hydroquinone to sustain gamma-carboxylation of many blood coagulation factors. Here, we report the 3.6 A crystal structure of a bacterial homologue of VKOR from Synechococcus sp. The structure shows VKOR in complex with its naturally fused redox partner, a thioredoxin-like domain, and corresponds to an arrested state of electron transfer. The catalytic core of VKOR is a four transmembrane helix bundle that surrounds a quinone, connected through an additional transmembrane segment with the periplasmic thioredoxin-like domain. We propose a pathway for how VKOR uses electrons from cysteines of newly synthesized proteins to reduce a quinone, a mechanism confirmed by in vitro reconstitution of vitamin K-dependent disulphide bridge formation. Our results have implications for the mechanism of the mammalian VKOR and explain how mutations can cause resistance to the VKOR inhibitor warfarin, the most commonly used oral anticoagulant.

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

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

1 Structural highlights
2 Evolutionary Conservation
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3kp8"

@@ Line 1: / Line 1: @@
 ==The thioredoxin-like domain of a VKOR homolog from Synechococcus sp.==
-<StructureSection load='3kp8' size='340' side='right' caption='[[3kp8]], [[Resolution|resolution]] 1.66&Aring;' scene=''>
+<StructureSection load='3kp8' size='340' side='right'caption='[[3kp8]], [[Resolution|resolution]] 1.66&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3kp8]] is a 1 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=3KP8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KP8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3kp8]] is a 1 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=3KP8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KP8 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3kp9|3kp9]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.66&#8491;</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'>[https://proteopedia.org/fgij/fg.htm?mol=3kp8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kp8 OCA], [https://pdbe.org/3kp8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kp8 RCSB], [https://www.ebi.ac.uk/pdbsum/3kp8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kp8 ProSAT]</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=3kp8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kp8 OCA], [http://pdbe.org/3kp8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kp8 RCSB], [http://www.ebi.ac.uk/pdbsum/3kp8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kp8 ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 13: / Line 12: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kp/3kp8_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 31: / Line 30: @@
 __TOC__
 </StructureSection>
-[[Category: Cyanobacteria bacterium yellowstone b']]
+[[Category: Large Structures]]
-[[Category: Beckwith, J]]
+[[Category: Beckwith J]]
-[[Category: Boyd, D]]
+[[Category: Boyd D]]
-[[Category: Dutton, R J]]
+[[Category: Dutton RJ]]
-[[Category: Li, W]]
+[[Category: Li W]]
-[[Category: Rapoport, T A]]
+[[Category: Rapoport TA]]
-[[Category: Schulman, S]]
+[[Category: Schulman S]]
-[[Category: Blood coagulation]]
-[[Category: Disulfide formation]]
-[[Category: Oxidoreductase]]
-[[Category: Redox partner]]

3kp8

From Proteopedia

Current revision

The thioredoxin-like domain of a VKOR homolog from Synechococcus sp.

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox