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4q73

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Revision as of 07:46, 8 February 2023

Crystal Structure of Bradyrhizobium japonicum Proline Utilization A (PutA) Mutant D778Y

Structural highlights

4q73 is a 2 chain structure with sequence from Bradyrhizobium diazoefficiens USDA 110. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q89E26_BRADU

Publication Abstract from PubMed

Proline utilization A from Bradyrhizobium japonicum (BjPutA) is a bifunctional flavoenzyme that catalyzes the oxidation of proline to glutamate using fused proline dehydrogenase (PRODH) and Delta1-pyrroline-5-carboxylate dehydrogenase (P5CDH) domains. Recent crystal structures and kinetic data suggest an intramolecular channel connects the two active sites, promoting substrate channeling of the intermediate Delta1-pyrroline-5-carboxylate/glutamate-gamma-semialdehyde (P5C/GSA). In this work, the structure of the channel was explored by inserting large side chain residues at four positions along the channel in BjPutA. Kinetic analysis of the different mutants revealed replacement of D779 with Tyr (D779Y) or Trp (D779W) significantly decreased the overall rate of the PRODH-P5CDH channeling reaction. X-ray crystal structures of D779Y and D779W revealed that the large side chains caused a constriction in the central section of the tunnel, thus likely impeding the travel of P5C/GSA in the channel. The D779Y and D779W mutants have PRODH activity similar to that of wild-type BjPutA but exhibit significantly lower P5CDH activity, suggesting that exogenous P5C/GSA enters the channel upstream of Asp779. Replacement of nearby Asp778 with Tyr (D778Y) did not impact BjPutA channeling activity. Consistent with the kinetic results, the X-ray crystal structure of D778Y shows that the main channel pathway is not impacted; however, an off-cavity pathway is closed off from the channel. These findings provide evidence that the off-cavity pathway is not essential for substrate channeling in BjPutA.

Kinetic and Structural Characterization of Tunnel-Perturbing Mutants in Bradyrhizobium japonicum Proline Utilization A.,Arentson BW, Luo M, Pemberton TA, Tanner JJ, Becker DF Biochemistry. 2014 Jul 30. PMID:25046425^[1]

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

References

↑ Arentson BW, Luo M, Pemberton TA, Tanner JJ, Becker DF. Kinetic and Structural Characterization of Tunnel-Perturbing Mutants in Bradyrhizobium japonicum Proline Utilization A. Biochemistry. 2014 Jul 30. PMID:25046425 doi:http://dx.doi.org/10.1021/bi5007404

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4q73"

Categories: Bradyrhizobium diazoefficiens USDA 110 | Large Structures | Luo M | Pemberton TA | Tanner JJ

@@ Line 3: / Line 3: @@
 <StructureSection load='4q73' size='340' side='right'caption='[[4q73]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4q73]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bradu Bradu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q73 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q73 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4q73]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bradyrhizobium_diazoefficiens_USDA_110 Bradyrhizobium diazoefficiens USDA 110]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q73 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q73 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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4q71|4q71]]</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=4q73 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q73 OCA], [https://pdbe.org/4q73 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q73 RCSB], [https://www.ebi.ac.uk/pdbsum/4q73 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q73 ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BJ6T_21270, blr7261, putA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224911 BRADU])</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=4q73 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q73 OCA], [http://pdbe.org/4q73 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4q73 RCSB], [http://www.ebi.ac.uk/pdbsum/4q73 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4q73 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q89E26_BRADU Q89E26_BRADU]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 25: @@
 __TOC__
 </StructureSection>
-[[Category: Bradu]]
+[[Category: Bradyrhizobium diazoefficiens USDA 110]]
 [[Category: Large Structures]]
-[[Category: Luo, M]]
+[[Category: Luo M]]
-[[Category: Pemberton, T A]]
+[[Category: Pemberton TA]]
-[[Category: Tanner, J J]]
+[[Category: Tanner JJ]]
-[[Category: 1-pyrroline-5-carboxylate dehydrogenase]]
-[[Category: Beta-alpha barrel]]
-[[Category: Fad binding]]
-[[Category: Oxidoreductase]]
-[[Category: Proline dehydrogenase]]
-[[Category: Proline utilization some]]
-[[Category: Puta]]
-[[Category: Rossmann fold]]

4q73

From Proteopedia

Revision as of 07:46, 8 February 2023

Crystal Structure of Bradyrhizobium japonicum Proline Utilization A (PutA) Mutant D778Y

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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