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.


5fb3

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:11, 20 March 2024) (edit) (undo)
 
(One intermediate revision not shown.)
Line 3: Line 3:
<StructureSection load='5fb3' size='340' side='right'caption='[[5fb3]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
<StructureSection load='5fb3' size='340' side='right'caption='[[5fb3]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[5fb3]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrcj Pyrcj]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FB3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FB3 FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[5fb3]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrobaculum_calidifontis_JCM_11548 Pyrobaculum calidifontis JCM 11548]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FB3 FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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]] 2.45&#8491;</td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">egsA, Pcal_0566 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=410359 PYRCJ])</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/sn-glycerol-1-phosphate_dehydrogenase sn-glycerol-1-phosphate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.261 1.1.1.261] </span></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=5fb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fb3 OCA], [https://pdbe.org/5fb3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fb3 RCSB], [https://www.ebi.ac.uk/pdbsum/5fb3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fb3 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=5fb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fb3 OCA], [http://pdbe.org/5fb3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fb3 RCSB], [http://www.ebi.ac.uk/pdbsum/5fb3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fb3 ProSAT]</span></td></tr>
+
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/G1PDH_PYRCJ G1PDH_PYRCJ]] Catalyzes the NAD(P)H-dependent reduction of dihydroxyacetonephosphate (DHAP or glycerone phosphate) to glycerol 1-phosphate (G1P). The G1P thus generated is used as the glycerophosphate backbone of phospholipids in the cellular membranes of Archaea.
+
[https://www.uniprot.org/uniprot/G1PDH_PYRCJ G1PDH_PYRCJ] Catalyzes the NAD(P)H-dependent reduction of dihydroxyacetonephosphate (DHAP or glycerone phosphate) to glycerol 1-phosphate (G1P). The G1P thus generated is used as the glycerophosphate backbone of phospholipids in the cellular membranes of Archaea.
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
A gene encoding an sn-glycerol-1-phosphate dehydrogenase (G1PDH) was identified in the hyperthermophilic archaeon Pyrobaculum calidifontis. The gene was overexpressed in Escherichia coli, and its product was purified and characterized. In contrast to conventional G1PDHs, the expressed enzyme showed strong preference for NADH: the reaction rate (Vmax ) with NADPH was only 2.4% of that with NADH. The crystal structure of the enzyme was determined at a resolution of 2.45 A. The asymmetric unit consisted of one homohexamer. Refinement of the structure and HPLC analysis showed the presence of the bound cofactor NADPH in subunits D, E, and F, even though it was not added in the crystallization procedure. The phosphate group at C2' of the adenine ribose of NADPH is tightly held through the five biased hydrogen bonds with Ser40 and Thr42. In comparison with the known G1PDH structure, the NADPH molecule was observed to be pushed away from the normal coenzyme binding site. Interestingly, the S40A/T42A double mutant enzyme acquired much higher reactivity than the wild-type enzyme with NADPH, which suggests that the biased interactions around the C2'-phosphate group make NADPH binding insufficient for catalysis. Our results provide a unique structural basis for coenzyme preference in NAD(P)-dependent dehydrogenases. Proteins 2016. (c) 2016 Wiley Periodicals, Inc.
+
-
 
+
-
Unique coenzyme binding mode of hyperthermophilic archaeal sn-glycerol-1-phosphate dehydrogenase from Pyrobaculum calidifontis.,Hayashi J, Yamamoto K, Yoneda K, Ohshima T, Sakuraba H Proteins. 2016 Sep 12. doi: 10.1002/prot.25161. PMID:27616573<ref>PMID:27616573</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 5fb3" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Pyrcj]]
+
[[Category: Pyrobaculum calidifontis JCM 11548]]
-
[[Category: Sn-glycerol-1-phosphate dehydrogenase]]
+
[[Category: Hayashi J]]
-
[[Category: Hayashi, J]]
+
[[Category: Ohshima T]]
-
[[Category: Ohshima, T]]
+
[[Category: Sakuraba H]]
-
[[Category: Sakuraba, H]]
+
[[Category: Yamamoto K]]
-
[[Category: Yamamoto, K]]
+
[[Category: Yoneda K]]
-
[[Category: Yoneda, K]]
+
-
[[Category: Oxidoreductase]]
+
-
[[Category: Rossmann fold]]
+

Current revision

Structure of glycerophosphate dehydrogenase in complex with NADPH

PDB ID 5fb3

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5fb3"
Personal tools