This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1bez

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

HALOALKANE DEHALOGENASE MUTANT WITH TRP 175 REPLACED BY TYR AT PH 5

Structural highlights

1bez is a 1 chain structure with sequence from Xanthobacter autotrophicus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DHLA_XANAU Catalyzes hydrolytic cleavage of carbon-halogen bonds in halogenated aliphatic compounds, leading to the formation of the corresponding primary alcohols, halide ions and protons. Has a broad substrate specificity, which includes terminally mono- and di- chlorinated and brominated alkanes (up to C4 only). The highest activity was found with 1,2-dichloroethane, 1,3-dichloropropane, and 1,2-dibromoethane.

Evolutionary Conservation

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

Publication Abstract from PubMed

Haloalkane dehalogenase (DhlA) catalyzes the hydrolysis of haloalkanes via an alkyl-enzyme intermediate. Trp175 forms a halogen/halide-binding site in the active-site cavity together with Trp125. To get more insight in the role of Trp175 in DhlA, we mutated residue 175 and explored the kinetics and X-ray structure of the Trp175Tyr enzyme. The mutagenesis study indicated that an aromatic residue at position 175 is important for the catalytic performance of DhlA. Pre-steady-state kinetic analysis of Trp175Tyr-DhlA showed that the observed 6-fold increase of the Km for 1,2-dibromoethane (DBE) results from reduced rates of both DBE binding and cleavage of the carbon-bromine bond. Furthermore, the enzyme isomerization preceding bromide release became 4-fold faster in the mutant enzyme. As a result, the rate of hydrolysis of the alkyl-enzyme intermediate became the main determinant of the kcat for DBE, which was 2-fold higher than the wild-type kcat. The X-ray structure of the mutant enzyme at pH 6 showed that the backbone structure of the enzyme remains intact and that the tyrosine side chain lies in the same plane as Trp175 in the wild-type enzyme. The Clalpha-stabilizing aromatic rings of Tyr175 and Trp125 are 0.7 A further apart and due to the smaller size of the mutated residue, the volume of the cavity has increased by one-fifth. X-ray structures of mutant and wild-type enzyme at pH 5 demonstrated that the Tyr175 side chain rotated away upon binding of an acetic acid molecule, leaving one of its oxygen atoms hydrogen bonded to the indole nitrogen of Trp125 only. These structural changes indicate a weakened interaction between residue 175 and the halogen atom or halide ion in the active site and help to explain the kinetic changes induced by the Trp175Tyr mutation.

Kinetic analysis and X-ray structure of haloalkane dehalogenase with a modified halide-binding site.,Krooshof GH, Ridder IS, Tepper AW, Vos GJ, Rozeboom HJ, Kalk KH, Dijkstra BW, Janssen DB Biochemistry. 1998 Oct 27;37(43):15013-23. PMID:9790663^[1]

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

References

↑ Krooshof GH, Ridder IS, Tepper AW, Vos GJ, Rozeboom HJ, Kalk KH, Dijkstra BW, Janssen DB. Kinetic analysis and X-ray structure of haloalkane dehalogenase with a modified halide-binding site. Biochemistry. 1998 Oct 27;37(43):15013-23. PMID:9790663 doi:10.1021/bi9815187

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1bez"

@@ Line 1: / Line 1: @@
 ==HALOALKANE DEHALOGENASE MUTANT WITH TRP 175 REPLACED BY TYR AT PH 5==
-<StructureSection load='1bez' size='340' side='right' caption='[[1bez]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='1bez' size='340' side='right'caption='[[1bez]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1bez]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"corynebacterium_autotrophicum"_baumgarten_et_al._1974 "corynebacterium autotrophicum" baumgarten et al. 1974]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BEZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BEZ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1bez]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthobacter_autotrophicus Xanthobacter autotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BEZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BEZ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</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]] 2.1&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Haloalkane_dehalogenase Haloalkane dehalogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.8.1.5 3.8.1.5] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene></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=1bez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bez OCA], [http://pdbe.org/1bez PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bez RCSB], [http://www.ebi.ac.uk/pdbsum/1bez PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1bez 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=1bez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bez OCA], [https://pdbe.org/1bez PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bez RCSB], [https://www.ebi.ac.uk/pdbsum/1bez PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bez ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DHLA_XANAU DHLA_XANAU]] Catalyzes hydrolytic cleavage of carbon-halogen bonds in halogenated aliphatic compounds, leading to the formation of the corresponding primary alcohols, halide ions and protons. Has a broad substrate specificity, which includes terminally mono- and di- chlorinated and brominated alkanes (up to C4 only). The highest activity was found with 1,2-dichloroethane, 1,3-dichloropropane, and 1,2-dibromoethane.
+[https://www.uniprot.org/uniprot/DHLA_XANAU DHLA_XANAU] Catalyzes hydrolytic cleavage of carbon-halogen bonds in halogenated aliphatic compounds, leading to the formation of the corresponding primary alcohols, halide ions and protons. Has a broad substrate specificity, which includes terminally mono- and di- chlorinated and brominated alkanes (up to C4 only). The highest activity was found with 1,2-dichloroethane, 1,3-dichloropropane, and 1,2-dibromoethane.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/be/1bez_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/be/1bez_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 29: / Line 29: @@
 </div>
 <div class="pdbe-citations 1bez" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Dehalogenase 3D structures|Dehalogenase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Corynebacterium autotrophicum baumgarten et al. 1974]]
+[[Category: Large Structures]]
-[[Category: Haloalkane dehalogenase]]
+[[Category: Xanthobacter autotrophicus]]
-[[Category: Dijkstra, B W]]
+[[Category: Dijkstra BW]]
-[[Category: Kalk, K H]]
+[[Category: Kalk KH]]
-[[Category: Ridder, I S]]
+[[Category: Ridder IS]]
-[[Category: Rozeboom, H J]]
+[[Category: Rozeboom HJ]]
-[[Category: Vos, G J]]
+[[Category: Vos GJ]]
-[[Category: Alpha/beta-hydrolase]]
-[[Category: Dehalogenase]]

1bez

From Proteopedia

Current revision

HALOALKANE DEHALOGENASE MUTANT WITH TRP 175 REPLACED BY TYR AT PH 5

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox