This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

5kms

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 06:57, 29 March 2023

The structure of type II NADH dehydrogenase from Caldalkalibacillus thermarum complexed with NAD+ at 2.5 angstrom resolution.

Structural highlights

5kms is a 4 chain structure with sequence from Caldalkalibacillus thermarum TA2.A1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

F5L3B8_CALTT

Publication Abstract from PubMed

Type II NADH:quinone oxidoreductase (NDH-2) is central to the respiratory chains of many organisms. It is not present in mammals so may be exploited as an antimicrobial drug target or used as a substitute for dysfunctional respiratory complex I in neuromuscular disorders. NDH-2 is a single-subunit monotopic membrane protein with just a flavin cofactor, yet no consensus exists on its mechanism. Here, we use steady-state and pre-steady-state kinetics combined with mutagenesis and structural studies to determine the mechanism of NDH-2 from Caldalkalibacillus thermarum. We show that the two substrate reactions occur independently, at different sites, and regardless of the occupancy of the partner site. We conclude that the reaction pathway is determined stochastically, by the substrate/product concentrations and dissociation constants, and can follow either a ping-pong or ternary mechanism. This mechanistic versatility provides a unified explanation for all extant data and a new foundation for the development of therapeutic strategies.

The mechanism of catalysis by type-II NADH:quinone oxidoreductases.,Blaza JN, Bridges HR, Aragao D, Dunn EA, Heikal A, Cook GM, Nakatani Y, Hirst J Sci Rep. 2017 Jan 9;7:40165. doi: 10.1038/srep40165. PMID:28067272^[1]

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

References

↑ Blaza JN, Bridges HR, Aragao D, Dunn EA, Heikal A, Cook GM, Nakatani Y, Hirst J. The mechanism of catalysis by type-II NADH:quinone oxidoreductases. Sci Rep. 2017 Jan 9;7:40165. doi: 10.1038/srep40165. PMID:28067272 doi:http://dx.doi.org/10.1038/srep40165

1 Structural highlights
2 Function
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/5kms"

Categories: Caldalkalibacillus thermarum TA2 A1 | Large Structures | Aragao D | Cook GM | Nakatani Y

@@ Line 3: / Line 3: @@
 <StructureSection load='5kms' size='340' side='right'caption='[[5kms]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5kms]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Caltt Caltt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KMS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5KMS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5kms]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Caldalkalibacillus_thermarum_TA2.A1 Caldalkalibacillus thermarum TA2.A1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KMS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KMS FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5kmq|5kmq]], [[5kmp|5kmp]], [[5kmr|5kmr]]</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=5kms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kms OCA], [https://pdbe.org/5kms PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kms RCSB], [https://www.ebi.ac.uk/pdbsum/5kms PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kms ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CathTA2_0279 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=986075 CALTT])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5kms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kms OCA], [http://pdbe.org/5kms PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kms RCSB], [http://www.ebi.ac.uk/pdbsum/5kms PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kms ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/F5L3B8_CALTT F5L3B8_CALTT]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Caltt]]
+[[Category: Caldalkalibacillus thermarum TA2 A1]]
 [[Category: Large Structures]]
-[[Category: Aragao, D]]
+[[Category: Aragao D]]
-[[Category: Cook, G M]]
+[[Category: Cook GM]]
-[[Category: Nakatani, Y]]
+[[Category: Nakatani Y]]
-[[Category: Nadh dehydrogenase]]
-[[Category: Oxidoreductase]]
-[[Category: Rossmann fold]]

5kms

From Proteopedia

Revision as of 06:57, 29 March 2023

The structure of type II NADH dehydrogenase from Caldalkalibacillus thermarum complexed with NAD+ at 2.5 angstrom resolution.

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox