1nzy: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
Line 3: Line 3:
<StructureSection load='1nzy' size='340' side='right'caption='[[1nzy]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='1nzy' size='340' side='right'caption='[[1nzy]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1nzy]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseuc Pseuc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NZY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NZY FirstGlance]. <br>
<table><tr><td colspan='2'>[[1nzy]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp._CBS3 Pseudomonas sp. CBS3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NZY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NZY FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCA:4-HYDROXYBENZOYL+COENZYME+A'>BCA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.8&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/4-chlorobenzoate_dehalogenase 4-chlorobenzoate dehalogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.8.1.6 3.8.1.6] </span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCA:4-HYDROXYBENZOYL+COENZYME+A'>BCA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=1nzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nzy OCA], [https://pdbe.org/1nzy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nzy RCSB], [https://www.ebi.ac.uk/pdbsum/1nzy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nzy ProSAT]</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=1nzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nzy OCA], [https://pdbe.org/1nzy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nzy RCSB], [https://www.ebi.ac.uk/pdbsum/1nzy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nzy ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/CBADH_PSEUC CBADH_PSEUC] Dehalogenates 4-chlorobenzoyl-CoA, 4-iodobenzoyl-CoA and 4-bromobenzoyl-CoA, but not 4-fluorobenzoyl-CoA. Inactive towards crotonyl-CoA, alpha-methylcrotonyl-CoA and beta-methylcrotonyl-CoA.<ref>PMID:1610806</ref> <ref>PMID:7579994</ref>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Line 18: Line 20:
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1nzy ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1nzy ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Here we describe the three-dimensional structure of 4-chlorobenzoyl-CoA dehalogenase from Pseudomonas sp. strain CBS-3. This enzyme catalyzes the hydrolysis of 4-chlorobenzoyl-CoA to 4-hydroxybenzoyl-CoA. The molecular structure of the enzyme/4-hydroxybenzoyl-CoA complex was solved by the techniques of multiple isomorphous replacement, solvent flattening, and molecular averaging. Least-squares refinement of the protein model reduced the crystallographic R factor to 18.8% for all measured X-ray data from 30 to 1.8 A resolution. The crystallographic investigation of this dehalogenase revealed that the enzyme is a trimer. Each subunit of the trimer folds into two distinct motifs. The larger, N-terminal domain is characterized by 10 strands of beta-pleated sheet that form two distinct layers which lie nearly perpendicular to one another. These layers of beta-sheet are flanked on either side by alpha-helices. The C-terminal domain extends away from the body of the molecule and is composed of three amphiphilic alpha-helices. This smaller domain is primarily involved in trimerization. The two domains of the subunit are linked together by a cation, most likely a calcium ion. The 4-hydroxybenzoyl-CoA molecule adopts a curved conformation within the active site such that the 4-hydroxybenzoyl and the adenosine moieties are buried while the pantothenate and pyrophosphate groups of the coenzyme are more solvent exposed. From the three-dimensional structure it is clear that Asp 145 provides the side-chain carboxylate group that adds to form the Meisenheimer intermediate and His 90 serves as the general base in the subsequent hydrolysis step. Many of the structural principles derived from this investigation may be directly applicable to other related enzymes such as crotonase.
Structure of 4-chlorobenzoyl coenzyme A dehalogenase determined to 1.8 A resolution: an enzyme catalyst generated via adaptive mutation.,Benning MM, Taylor KL, Liu R-Q, Yang G, Xiang H, Wesenberg G, Dunaway-Mariano D, Holden HM Biochemistry. 1996 Jun 25;35(25):8103-9. PMID:8679561<ref>PMID:8679561</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1nzy" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
Line 34: Line 27:
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: 4-chlorobenzoate dehalogenase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Pseuc]]
[[Category: Pseudomonas sp. CBS3]]
[[Category: Benning, M M]]
[[Category: Benning MM]]
[[Category: Holden, H M]]
[[Category: Holden HM]]
[[Category: Lyase]]

Latest revision as of 11:00, 14 February 2024

4-CHLOROBENZOYL COENZYME A DEHALOGENASE FROM PSEUDOMONAS SP. STRAIN CBS-34-CHLOROBENZOYL COENZYME A DEHALOGENASE FROM PSEUDOMONAS SP. STRAIN CBS-3

Structural highlights

1nzy is a 3 chain structure with sequence from Pseudomonas sp. CBS3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.8Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CBADH_PSEUC Dehalogenates 4-chlorobenzoyl-CoA, 4-iodobenzoyl-CoA and 4-bromobenzoyl-CoA, but not 4-fluorobenzoyl-CoA. Inactive towards crotonyl-CoA, alpha-methylcrotonyl-CoA and beta-methylcrotonyl-CoA.[1] [2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Chang KH, Liang PH, Beck W, Scholten JD, Dunaway-Mariano D. Isolation and characterization of the three polypeptide components of 4-chlorobenzoate dehalogenase from Pseudomonas sp. strain CBS-3. Biochemistry. 1992 Jun 23;31(24):5605-10. PMID:1610806
  2. ↑ Löffler F, Lingens F, Müller R. Dehalogenation of 4-chlorobenzoate. Characterisation of 4-chlorobenzoyl-coenzyme A dehalogenase from Pseudomonas sp. CBS3. Biodegradation. 1995 Sep;6(3):203-12. PMID:7579994 doi:10.1007/BF00700458

1nzy, resolution 1.80Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1nzy&oldid=4052750"