5kf6: Difference between revisions
No edit summary |
No edit summary |
||
| (2 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
==Structure of proline utilization A from Sinorhizobium meliloti complexed with L-tetrahydrofuroic acid and NAD+ in space group P21== | ==Structure of proline utilization A from Sinorhizobium meliloti complexed with L-tetrahydrofuroic acid and NAD+ in space group P21== | ||
<StructureSection load='5kf6' size='340' side='right' caption='[[5kf6]], [[Resolution|resolution]] 1.70Å' scene=''> | <StructureSection load='5kf6' size='340' side='right'caption='[[5kf6]], [[Resolution|resolution]] 1.70Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5kf6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KF6 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[5kf6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sinorhizobium_meliloti_SM11 Sinorhizobium meliloti SM11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KF6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KF6 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=TFB:TETRAHYDROFURAN-2-CARBOXYLIC+ACID'>TFB</scene> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7Å</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=TFB:TETRAHYDROFURAN-2-CARBOXYLIC+ACID'>TFB</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5kf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kf6 OCA], [https://pdbe.org/5kf6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kf6 RCSB], [https://www.ebi.ac.uk/pdbsum/5kf6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kf6 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/F7X6I3_SINMM F7X6I3_SINMM] Oxidizes proline to glutamate for use as a carbon and nitrogen source.[PIRNR:PIRNR000197] | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Aldehyde dehydrogenases (ALDHs) catalyze the NAD(P)+-dependent oxidation of aldehydes to carboxylic acids and are important for metabolism and detoxification. Although the ALDH superfamily fold is well established, some ALDHs contain an uncharacterized domain of unknown function (DUF) near the C-terminus of the polypeptide chain. Herein, we report the first structure of a protein containing the ALDH superfamily DUF. Proline utilization A from Sinorhizobium meliloti (SmPutA) is a 1233-residue bifunctional enzyme that contains the DUF in addition to proline dehydrogenase and L-glutamate-gamma-semialdehyde dehydrogenase catalytic modules. Structures of SmPutA with a proline analog bound to the proline dehydrogenase site and NAD+ bound to the ALDH site were determined in two space groups at 1.7 - 1.9 A resolution. The DUF consists of a Rossmann dinucleotide-binding fold fused to a 3-stranded beta-flap. The Rossmann domain resembles the classic ALDH superfamily NAD+-binding domain, while the flap is strikingly similar to the ALDH superfamily dimerization domain. Paradoxically, neither structural element performs its implied function. Electron density maps show that NAD+ does not bind to the DUF Rossmann fold. And small-angle X-ray scattering reveals a novel dimer that has never been seen in the ALDH superfamily. The structure suggests that the DUF is an adapter domain that stabilizes the aldehyde substrate binding loop and seals the substrate-channeling tunnel via tertiary structural interactions that mimic the quaternary structural interactions found in non-DUF PutAs. Kinetic data for SmPutA indicate a substrate-channeling mechanism, in agreement with previous studies of other PutAs. | |||
Structures of Proline Utilization A Reveal the Fold and Functions of the Aldehyde Dehydrogenase Superfamily Domain of Unknown Function.,Luo M, Gamage TT, Arentson BW, Schlasner KN, Becker DF, Tanner JJ J Biol Chem. 2016 Sep 27. pii: jbc.M116.756965. PMID:27679491<ref>PMID:27679491</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 5kf6" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Proline utilization A|Proline utilization A]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Sinorhizobium meliloti SM11]] | ||
[[Category: | [[Category: Tanner JJ]] | ||
Latest revision as of 12:59, 27 September 2023
Structure of proline utilization A from Sinorhizobium meliloti complexed with L-tetrahydrofuroic acid and NAD+ in space group P21Structure of proline utilization A from Sinorhizobium meliloti complexed with L-tetrahydrofuroic acid and NAD+ in space group P21
Structural highlights
FunctionF7X6I3_SINMM Oxidizes proline to glutamate for use as a carbon and nitrogen source.[PIRNR:PIRNR000197] Publication Abstract from PubMedAldehyde dehydrogenases (ALDHs) catalyze the NAD(P)+-dependent oxidation of aldehydes to carboxylic acids and are important for metabolism and detoxification. Although the ALDH superfamily fold is well established, some ALDHs contain an uncharacterized domain of unknown function (DUF) near the C-terminus of the polypeptide chain. Herein, we report the first structure of a protein containing the ALDH superfamily DUF. Proline utilization A from Sinorhizobium meliloti (SmPutA) is a 1233-residue bifunctional enzyme that contains the DUF in addition to proline dehydrogenase and L-glutamate-gamma-semialdehyde dehydrogenase catalytic modules. Structures of SmPutA with a proline analog bound to the proline dehydrogenase site and NAD+ bound to the ALDH site were determined in two space groups at 1.7 - 1.9 A resolution. The DUF consists of a Rossmann dinucleotide-binding fold fused to a 3-stranded beta-flap. The Rossmann domain resembles the classic ALDH superfamily NAD+-binding domain, while the flap is strikingly similar to the ALDH superfamily dimerization domain. Paradoxically, neither structural element performs its implied function. Electron density maps show that NAD+ does not bind to the DUF Rossmann fold. And small-angle X-ray scattering reveals a novel dimer that has never been seen in the ALDH superfamily. The structure suggests that the DUF is an adapter domain that stabilizes the aldehyde substrate binding loop and seals the substrate-channeling tunnel via tertiary structural interactions that mimic the quaternary structural interactions found in non-DUF PutAs. Kinetic data for SmPutA indicate a substrate-channeling mechanism, in agreement with previous studies of other PutAs. Structures of Proline Utilization A Reveal the Fold and Functions of the Aldehyde Dehydrogenase Superfamily Domain of Unknown Function.,Luo M, Gamage TT, Arentson BW, Schlasner KN, Becker DF, Tanner JJ J Biol Chem. 2016 Sep 27. pii: jbc.M116.756965. PMID:27679491[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||