5ur2: Difference between revisions
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The | ==Crystal structure of proline utilization A (PutA) from Bdellovibrio bacteriovorus inactivated by N-propargylglycine== | ||
<StructureSection load='5ur2' size='340' side='right'caption='[[5ur2]], [[Resolution|resolution]] 2.23Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5ur2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bdellovibrio_bacteriovorus_HD100 Bdellovibrio bacteriovorus HD100]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UR2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UR2 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.23Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=P5F:N-PROPARGYLGLYCINE-MODIFIED+FLAVIN+ADENINE+DINUCLEOTIDE'>P5F</scene></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=5ur2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ur2 OCA], [https://pdbe.org/5ur2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ur2 RCSB], [https://www.ebi.ac.uk/pdbsum/5ur2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ur2 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q6MNK1_BDEBA Q6MNK1_BDEBA] Oxidizes proline to glutamate for use as a carbon and nitrogen source.[PIRNR:PIRNR000197] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Many enzymes form homooligomers, yet the functional significance of self-association is seldom obvious. Herein, we examine the connection between oligomerization and catalytic function for proline utilization A (PutA) enzymes. PutAs are bifunctional enzymes that catalyze both reactions of proline catabolism. Type A PutAs are the smallest members of the family, possessing a minimal domain architecture consisting of N-terminal proline dehydrogenase and C-terminal l-glutamate-gamma-semialdehyde dehydrogenase modules. Type A PutAs form domain-swapped dimers, and in one case (Bradyrhizobium japonicum PutA), two of the dimers assemble into a ring-shaped tetramer. Whereas the dimer has a clear role in substrate channeling, the functional significance of the tetramer is unknown. To address this question, we performed structural studies of four-type A PutAs from two clades of the PutA tree. The crystal structure of Bdellovibrio bacteriovorus PutA covalently inactivated by N-propargylglycine revealed a fold and substrate-channeling tunnel similar to other PutAs. Small-angle X-ray scattering (SAXS) and analytical ultracentrifugation indicated that Bdellovibrio PutA is dimeric in solution, in contrast to the prediction from crystal packing of a stable tetrameric assembly. SAXS studies of two other type A PutAs from separate clades also suggested that the dimer predominates in solution. To assess whether the tetramer of B. japonicum PutA is necessary for catalytic function, a hot spot disruption mutant that cleanly produces dimeric protein was generated. The dimeric variant exhibited kinetic parameters similar to the wild-type enzyme. These results implicate the domain-swapped dimer as the core structural and functional unit of type A PutAs. ENZYMES: Proline dehydrogenase (EC 1.5.5.2); l-glutamate-gamma-semialdehyde dehydrogenase (EC 1.2.1.88). DATABASES: The atomic coordinates and structure factor amplitudes have been deposited in the Protein Data Bank under accession number 5UR2. The SAXS data have been deposited in the SASBDB under the following accession codes: SASDCP3 (BbPutA), SASDCQ3 (DvPutA 1.5 mg.mL-1 ), SASDCX3 (DvPutA 3.0 mg.mL-1 ), SASDCY3 (DvPutA 4.5 mg.mL-1 ), SASDCR3 (LpPutA 3.0 mg.mL-1 ), SASDCV3 (LpPutA 5.0 mg.mL-1 ), SASDCW3 (LpPutA 8.0 mg.mL-1 ), SASDCS3 (BjPutA 2.3 mg.mL-1 ), SASDCT3 (BjPutA 4.7 mg.mL-1 ), SASDCU3 (BjPutA 7.0 mg.mL-1 ), SASDCZ3 (R51E 2.3 mg.mL-1 ), SASDC24 (R51E 4.7 mg.mL-1 ), SASDC34 (R51E 7.0 mg.mL-1 ). | |||
Biophysical investigation of type A PutAs reveals a conserved core oligomeric structure.,Korasick DA, Singh H, Pemberton TA, Luo M, Dhatwalia R, Tanner JJ FEBS J. 2017 Jul 15. doi: 10.1111/febs.14165. PMID:28710792<ref>PMID:28710792</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: Tanner | <div class="pdbe-citations 5ur2" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Proline utilization A|Proline utilization A]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Bdellovibrio bacteriovorus HD100]] | |||
[[Category: Large Structures]] | |||
[[Category: Tanner JJ]] | |||