|
|
| (3 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | + | |
| | ==Crystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA reduced with dithionite== | | ==Crystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA reduced with dithionite== |
| - | <StructureSection load='4nmd' size='340' side='right' caption='[[4nmd]], [[Resolution|resolution]] 1.98Å' scene=''> | + | <StructureSection load='4nmd' size='340' side='right'caption='[[4nmd]], [[Resolution|resolution]] 1.98Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4nmd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Geosl Geosl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NMD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NMD FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4nmd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacter_sulfurreducens_PCA Geobacter sulfurreducens PCA]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NMD FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FDA:DIHYDROFLAVINE-ADENINE+DINUCLEOTIDE'>FDA</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]] 1.979Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4nm9|4nm9]], [[4nma|4nma]], [[4nmb|4nmb]], [[4nmc|4nmc]], [[4nme|4nme]], [[4nmf|4nmf]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FDA:DIHYDROFLAVINE-ADENINE+DINUCLEOTIDE'>FDA</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">putA, GSU3395 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243231 GEOSL])</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=4nmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nmd OCA], [https://pdbe.org/4nmd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nmd RCSB], [https://www.ebi.ac.uk/pdbsum/4nmd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nmd 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=4nmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nmd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nmd RCSB], [http://www.ebi.ac.uk/pdbsum/4nmd PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q746X3_GEOSL Q746X3_GEOSL] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 16: |
Line 18: |
| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4nmd" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Proline utilization A|Proline utilization A]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Geosl]] | + | [[Category: Geobacter sulfurreducens PCA]] |
| - | [[Category: Singh, H]] | + | [[Category: Large Structures]] |
| - | [[Category: Tanner, J J]] | + | [[Category: Singh H]] |
| - | [[Category: Aldehyde dehydrogenase]] | + | [[Category: Tanner JJ]] |
| - | [[Category: Bifunctional enzyme]]
| + | |
| - | [[Category: Flavin adenine dinucleotide]]
| + | |
| - | [[Category: Flavoenzyme]]
| + | |
| - | [[Category: Nicotinamide adenine dinucleotide]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Proline catabolism]]
| + | |
| - | [[Category: Rossmann fold]]
| + | |
| - | [[Category: Substrate channeling]]
| + | |
| Structural highlights
Function
Q746X3_GEOSL
Publication Abstract from PubMed
Proline utilization A (PutA) proteins are bifunctional peripheral membrane flavoenzymes that catalyze the oxidation of l-proline to l-glutamate by the sequential activities of proline dehydrogenase and aldehyde dehydrogenase domains. Located at the inner membrane of Gram-negative bacteria, PutAs play a major role in energy metabolism by coupling the oxidation of proline imported from the environment to the reduction of membrane-associated quinones. Here, we report seven crystal structures of the 1,004-residue PutA from Geobacter sulfurreducens, along with determination of the protein oligomeric state by small-angle X-ray scattering and kinetic characterization of substrate channeling and quinone reduction. The structures reveal an elaborate and dynamic tunnel system featuring a 75-A-long tunnel that links the two active sites and six smaller tunnels that connect the main tunnel to the bulk medium. The locations of these tunnels and their responses to ligand binding and flavin reduction suggest hypotheses about how proline, water, and quinones enter the tunnel system and where l-glutamate exits. Kinetic measurements show that glutamate production from proline occurs without a lag phase, consistent with substrate channeling and implying that the observed tunnel is functionally relevant. Furthermore, the structure of reduced PutA complexed with menadione bisulfite reveals the elusive quinone-binding site. The benzoquinone binds within 4.0 A of the flavin si face, consistent with direct electron transfer. The location of the quinone site implies that the concave surface of the PutA dimer approaches the membrane. Altogether, these results provide insight into how PutAs couple proline oxidation to quinone reduction.
Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site.,Singh H, Arentson BW, Becker DF, Tanner JJ Proc Natl Acad Sci U S A. 2014 Mar 4;111(9):3389-94. doi:, 10.1073/pnas.1321621111. Epub 2014 Feb 18. PMID:24550478[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Singh H, Arentson BW, Becker DF, Tanner JJ. Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site. Proc Natl Acad Sci U S A. 2014 Mar 4;111(9):3389-94. doi:, 10.1073/pnas.1321621111. Epub 2014 Feb 18. PMID:24550478 doi:http://dx.doi.org/10.1073/pnas.1321621111
|
