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.

2edc

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 07:06, 29 November 2017

CRYSTALLOGRAPHIC AND FLUORESCENCE STUDIES OF THE INTERACTION OF HALOALKANE DEHALOGENASE WITH HALIDE IONS: STUDIES WITH HALIDE COMPOUNDS REVEAL A HALIDE BINDING SITE IN THE ACTIVE SITE

Structural highlights

2edc is a 1 chain structure with sequence from "corynebacterium_autotrophicum"_baumgarten_et_al._1974 "corynebacterium autotrophicum" baumgarten et al. 1974. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Activity:	Haloalkane dehalogenase, with EC number 3.8.1.5
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 from Xanthobacter autotrophicus GJ10 catalyzes the conversion of 1,2-dichloroethane to 2-chloroethanol and chloride without use of oxygen or cofactors. The active site is situated in an internal cavity, which is accessible from the solvent, even in the crystal. Crystal structures of the dehalogenase enzyme complexed with iodoacetamide, chloroacetamide, iodide, and chloride at pH 6.2 and 8.2 revealed a halide binding site between the ring NH's of two tryptophan residues, Trp-125 and Trp-175, located in the active site. The halide ion lies on the intersection of the planes of the rings of the tryptophans. The binding of iodide and chloride to haloalkane dehalogenase caused a strong decrease in protein fluorescence. The decrease could be fitted to a modified form of the Stern-Volmer equation, indicating the presence of fluorophors of different accessibilities. Halide binding was much stronger at pH 6.0 than at pH 8.2. Assuming ligand binding to Trp-125 and Trp-175 as the sole cause of fluorescence quenching, dissociation constants at pH 6.0 with chloride and iodide were calculated to be 0.49 +/- 0.04 and 0.074 +/- 0.007 mM, respectively. Detailed structural investigation showed that the halide binding site probably stabilizes the halide product as well as the negatively charged transition state occurring during the formation of the covalent intermediate.

Crystallographic and fluorescence studies of the interaction of haloalkane dehalogenase with halide ions. Studies with halide compounds reveal a halide binding site in the active site.,Verschueren KH, Kingma J, Rozeboom HJ, Kalk KH, Janssen DB, Dijkstra BW Biochemistry. 1993 Sep 7;32(35):9031-7. PMID:8369276^[1]

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

References

↑ Verschueren KH, Kingma J, Rozeboom HJ, Kalk KH, Janssen DB, Dijkstra BW. Crystallographic and fluorescence studies of the interaction of haloalkane dehalogenase with halide ions. Studies with halide compounds reveal a halide binding site in the active site. Biochemistry. 1993 Sep 7;32(35):9031-7. PMID:8369276

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2edc"

Categories: Corynebacterium autotrophicum baumgarten et al. 1974 | Haloalkane dehalogenase | Dijkstra, B W | Verschueren, K H.G | Dehalogenase

@@ Line 1: / Line 1: @@
 ==CRYSTALLOGRAPHIC AND FLUORESCENCE STUDIES OF THE INTERACTION OF HALOALKANE DEHALOGENASE WITH HALIDE IONS: STUDIES WITH HALIDE COMPOUNDS REVEAL A HALIDE BINDING SITE IN THE ACTIVE SITE==
 <StructureSection load='2edc' size='340' side='right' caption='[[2edc]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
@@ Line 5: / Line 6: @@
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></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='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=2edc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2edc OCA], [http://pdbe.org/2edc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2edc RCSB], [http://www.ebi.ac.uk/pdbsum/2edc PDBsum]</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=2edc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2edc OCA], [http://pdbe.org/2edc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2edc RCSB], [http://www.ebi.ac.uk/pdbsum/2edc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2edc ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 17: / Line 18: @@
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</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/chain_selection.php?pdb_ID=2ata 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=2edc ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 29: @@
 </div>
 <div class="pdbe-citations 2edc" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[Dehalogenase|Dehalogenase]]
 == References ==
 <references/>

2edc

From Proteopedia

Revision as of 07:06, 29 November 2017

CRYSTALLOGRAPHIC AND FLUORESCENCE STUDIES OF THE INTERACTION OF HALOALKANE DEHALOGENASE WITH HALIDE IONS: STUDIES WITH HALIDE COMPOUNDS REVEAL A HALIDE BINDING SITE IN THE ACTIVE SITE

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox