1kc3

From Proteopedia

(Difference between revisions)

Revision as of 06:51, 11 August 2021

Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH and dTDP-L-rhamnose

Structural highlights

1kc3 is a 1 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	1kbz, 1kc0, 1kc1
Activity:	dTDP-4-dehydrorhamnose reductase, with EC number 1.1.1.133
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RMLD_SALTY] Catalyzes the reduction of dTDP-6-deoxy-L-lyxo-4-hexulose to yield dTDP-L-rhamnose. RmlD uses NADH and NADPH nearly equally well.

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

dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) catalyzes the final step in the conversion of dTDP-D-glucose to dTDP-L-rhamnose in an NAD(P)H- and Mg2+-dependent reaction. L-rhamnose biosynthesis is an antibacterial target. The structure of RmlD from Salmonella enterica serovar Typhimurium has been determined, and complexes with NADH, NADPH, and dTDP-L-rhamnose are reported. RmlD differs from other short chain dehydrogenases in that it has a novel dimer interface that contains Mg2+. Enzyme catalysis involves hydride transfer from the nicotinamide ring of the cofactor to the C4'-carbonyl group of the substrate. The substrate is activated through protonation by a conserved tyrosine. NAD(P)H is bound in a solvent-exposed cleft, allowing facile replacement. We suggest a novel role for the conserved serine/threonine residue of the catalytic triad of SDR enzymes.

Variation on a theme of SDR. dTDP-6-deoxy-L- lyxo-4-hexulose reductase (RmlD) shows a new Mg2+-dependent dimerization mode.,Blankenfeldt W, Kerr ID, Giraud MF, McMiken HJ, Leonard G, Whitfield C, Messner P, Graninger M, Naismith JH Structure. 2002 Jun;10(6):773-86. PMID:12057193^[1]

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

References

↑ Blankenfeldt W, Kerr ID, Giraud MF, McMiken HJ, Leonard G, Whitfield C, Messner P, Graninger M, Naismith JH. Variation on a theme of SDR. dTDP-6-deoxy-L- lyxo-4-hexulose reductase (RmlD) shows a new Mg2+-dependent dimerization mode. Structure. 2002 Jun;10(6):773-86. PMID:12057193

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1kc3"

@@ Line 3: / Line 3: @@
 <StructureSection load='1kc3' size='340' side='right'caption='[[1kc3]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1kc3]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KC3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KC3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1kc3]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KC3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KC3 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=TRH:2-DEOXY-THYMIDINE-BETA-L-RHAMNOSE'>TRH</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=TRH:2-DEOXY-THYMIDINE-BETA-L-RHAMNOSE'>TRH</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kbz|1kbz]], [[1kc0|1kc0]], [[1kc1|1kc1]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1kbz|1kbz]], [[1kc0|1kc0]], [[1kc1|1kc1]]</div></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dTDP-4-dehydrorhamnose_reductase dTDP-4-dehydrorhamnose reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.133 1.1.1.133] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/dTDP-4-dehydrorhamnose_reductase dTDP-4-dehydrorhamnose reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.133 1.1.1.133] </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=1kc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kc3 OCA], [http://pdbe.org/1kc3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kc3 RCSB], [http://www.ebi.ac.uk/pdbsum/1kc3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kc3 ProSAT]</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=1kc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kc3 OCA], [https://pdbe.org/1kc3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kc3 RCSB], [https://www.ebi.ac.uk/pdbsum/1kc3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kc3 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RMLD_SALTY RMLD_SALTY]] Catalyzes the reduction of dTDP-6-deoxy-L-lyxo-4-hexulose to yield dTDP-L-rhamnose. RmlD uses NADH and NADPH nearly equally well.
+[[https://www.uniprot.org/uniprot/RMLD_SALTY RMLD_SALTY]] Catalyzes the reduction of dTDP-6-deoxy-L-lyxo-4-hexulose to yield dTDP-L-rhamnose. RmlD uses NADH and NADPH nearly equally well.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]

1kc3

From Proteopedia

Revision as of 06:51, 11 August 2021

Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH and dTDP-L-rhamnose

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox