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5k3e

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Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/Glycolate - Cocrystallized

Structural highlights

5k3e is a 2 chain structure with sequence from Rhodopseudomonas palustris CGA009. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.54Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DEHA_RHOPA Catalyzes the hydrolytic defluorination of fluoroacetate to produce glycolate. Has lower activity towards bromoacetate and chloroacetate.^[1] ^[2]

Publication Abstract from PubMed

Freeze-trapping x-ray crystallography, nuclear magnetic resonance, and computational techniques reveal the distribution of states and their interconversion rates along the reaction pathway of a bacterial homodimeric enzyme, fluoroacetate dehalogenase (FAcD). The crystal structure of apo-FAcD exhibits asymmetry around the dimer interface and cap domain, priming one protomer for substrate binding. This asymmetry is dynamically averaged through conformational exchange on a millisecond time scale. During catalysis, the protomer conformational exchange rate becomes enhanced, the empty protomer exhibits increased local disorder, and water egresses. Computational studies identify allosteric pathways between protomers. Water release and enhanced dynamics associated with catalysis compensate for entropic losses from substrate binding while facilitating sampling of the transition state. The studies provide insights into how substrate-coupled allosteric modulation of structure and dynamics facilitates catalysis in a homodimeric enzyme.

The role of dimer asymmetry and protomer dynamics in enzyme catalysis.,Kim TH, Mehrabi P, Ren Z, Sljoka A, Ing C, Bezginov A, Ye L, Pomes R, Prosser RS, Pai EF Science. 2017 Jan 20;355(6322). pii: eaag2355. doi: 10.1126/science.aag2355. PMID:28104837^[3]

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

References

↑ Chan PW, Yakunin AF, Edwards EA, Pai EF. Mapping the Reaction Coordinates of Enzymatic Defluorination. J Am Chem Soc. 2011 Apr 21. PMID:21510690 doi:10.1021/ja200277d
↑ Chan PW, Yakunin AF, Edwards EA, Pai EF. Mapping the Reaction Coordinates of Enzymatic Defluorination. J Am Chem Soc. 2011 Apr 21. PMID:21510690 doi:10.1021/ja200277d
↑ Kim TH, Mehrabi P, Ren Z, Sljoka A, Ing C, Bezginov A, Ye L, Pomes R, Prosser RS, Pai EF. The role of dimer asymmetry and protomer dynamics in enzyme catalysis. Science. 2017 Jan 20;355(6322). pii: eaag2355. doi: 10.1126/science.aag2355. PMID:28104837 doi:http://dx.doi.org/10.1126/science.aag2355

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/5k3e"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/Glycolate - Cocrystallized==
-<StructureSection load='5k3e' size='340' side='right' caption='[[5k3e]], [[Resolution|resolution]] 1.54&Aring;' scene=''>
+<StructureSection load='5k3e' size='340' side='right'caption='[[5k3e]], [[Resolution|resolution]] 1.54&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5k3e]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K3E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K3E FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5k3e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodopseudomonas_palustris_CGA009 Rhodopseudomonas palustris CGA009]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K3E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K3E FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOA:GLYCOLIC+ACID'>GOA</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]] 1.54&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5k3a|5k3a]], [[5k3b|5k3b]], [[5k3c|5k3c]], [[5k3d|5k3d]], [[5k3f|5k3f]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOA:GLYCOLIC+ACID'>GOA</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Haloacetate_dehalogenase Haloacetate dehalogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.8.1.3 3.8.1.3] </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=5k3e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3e OCA], [https://pdbe.org/5k3e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k3e RCSB], [https://www.ebi.ac.uk/pdbsum/5k3e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3e 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=5k3e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3e OCA], [http://pdbe.org/5k3e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k3e RCSB], [http://www.ebi.ac.uk/pdbsum/5k3e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3e ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DEHA_RHOPA DEHA_RHOPA]] Catalyzes the hydrolytic defluorination of fluoroacetate to produce glycolate. Has lower activity towards bromoacetate and chloroacetate.<ref>PMID:21510690</ref> <ref>PMID:21510690</ref>
+[https://www.uniprot.org/uniprot/DEHA_RHOPA DEHA_RHOPA] Catalyzes the hydrolytic defluorination of fluoroacetate to produce glycolate. Has lower activity towards bromoacetate and chloroacetate.<ref>PMID:21510690</ref> <ref>PMID:21510690</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 19: @@
 </div>
 <div class="pdbe-citations 5k3e" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Dehalogenase 3D structures|Dehalogenase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Haloacetate dehalogenase]]
+[[Category: Large Structures]]
-[[Category: Kim, T H]]
+[[Category: Rhodopseudomonas palustris CGA009]]
-[[Category: Mehrabi, P]]
+[[Category: Kim TH]]
-[[Category: Pai, E F]]
+[[Category: Mehrabi P]]
-[[Category: Prosser, S R]]
+[[Category: Pai EF]]
-[[Category: Dehalogenase]]
+[[Category: Prosser SR]]
-[[Category: Homodimer]]
-[[Category: Hydrolase]]

5k3e

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Current revision

Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/Glycolate - Cocrystallized

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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