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.

6owm

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Horse liver F93W alcohol dehydrogenase complexed with NAD and pentafluorobenzyl alcohol

Structural highlights

6owm is a 2 chain structure with sequence from Equus caballus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.1Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ADH1E_HORSE

Publication Abstract from PubMed

Previous studies showed that the L57F and F93W alcohol dehydrogenases catalyze the oxidation of benzyl alcohol with some quantum mechanical hydrogen tunneling, whereas the V203A enzyme has diminished tunneling. Here, steady-state kinetics for the L57F and F93W enzymes were studied, and microscopic rate constants for the ordered bi-bi mechanism were estimated from simulations of transient kinetics for the S48T, F93A, S48T/F93A, F93W, and L57F enzymes. Catalytic efficiencies for benzyl alcohol oxidation (V1/EtKb) vary over a range of approximately 100-fold for the less active enzymes up to the L57F enzyme and are mostly associated with the binding of alcohol rather than the rate constants for hydride transfer. In contrast, catalytic efficiencies for benzaldehyde reduction (V2/EtKp) are approximately 500-fold higher for the L57F enzyme than for the less active enzymes and are mostly associated with the rate constants for hydride transfer. Atomic-resolution structures (1.1 A) for the F93W and L57F enzymes complexed with NAD(+) and 2,3,4,5,6-pentafluorobenzyl alcohol or 2,2,2-trifluoroethanol are almost identical to previous structures for the wild-type, S48T, and V203A enzymes. Least-squares refinement with SHELXL shows that the nicotinamide ring is slightly strained in all complexes and that the apparent donor-acceptor distances from C4N of NAD to C7 of pentafluorobenzyl alcohol range from 3.28 to 3.49 A (+/-0.02 A) and are not correlated with the rate constants for hydride transfer or hydrogen tunneling. How the substitutions affect the dynamics of reorganization during hydrogen transfer and the extent of tunneling remain to be determined.

Substitutions of Amino Acid Residues in the Substrate Binding Site of Horse Liver Alcohol Dehydrogenase Have Small Effects on the Structures but Significantly Affect Catalysis of Hydrogen Transfer.,Kim K, Plapp BV Biochemistry. 2020 Feb 10. doi: 10.1021/acs.biochem.9b01074. PMID:31994873^[1]

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

References

↑ Kim K, Plapp BV. Substitutions of Amino Acid Residues in the Substrate Binding Site of Horse Liver Alcohol Dehydrogenase Have Small Effects on the Structures but Significantly Affect Catalysis of Hydrogen Transfer. Biochemistry. 2020 Feb 10. doi: 10.1021/acs.biochem.9b01074. PMID:31994873 doi:http://dx.doi.org/10.1021/acs.biochem.9b01074

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/6owm"

Categories: Equus caballus | Large Structures | Plapp BV

@@ Line 3: / Line 3: @@
 <StructureSection load='6owm' size='340' side='right'caption='[[6owm]], [[Resolution|resolution]] 1.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6owm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OWM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OWM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6owm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OWM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OWM FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=NAJ:NICOTINAMIDE-ADENINE-DINUCLEOTIDE+(ACIDIC+FORM)'>NAJ</scene>, <scene name='pdbligand=PFB:2,3,4,5,6-PENTAFLUOROBENZYL+ALCOHOL'>PFB</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.1&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4dwv|4dwv]], [[1a71|1a71]], [[1axe|1axe]], [[6o91|6o91]], [[5kcp|5kcp]], [[4ng5|4ng5]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=NAJ:NICOTINAMIDE-ADENINE-DINUCLEOTIDE+(ACIDIC+FORM)'>NAJ</scene>, <scene name='pdbligand=PFB:2,3,4,5,6-PENTAFLUOROBENZYL+ALCOHOL'>PFB</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alcohol_dehydrogenase Alcohol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.1 1.1.1.1] </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=6owm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6owm OCA], [https://pdbe.org/6owm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6owm RCSB], [https://www.ebi.ac.uk/pdbsum/6owm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6owm 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=6owm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6owm OCA], [http://pdbe.org/6owm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6owm RCSB], [http://www.ebi.ac.uk/pdbsum/6owm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6owm ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/ADH1E_HORSE ADH1E_HORSE]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 19: @@
 </div>
 <div class="pdbe-citations 6owm" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Alcohol dehydrogenase 3D structures|Alcohol dehydrogenase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Alcohol dehydrogenase]]
 [[Category: Equus caballus]]
 [[Category: Large Structures]]
-[[Category: Plapp, B V]]
+[[Category: Plapp BV]]
-[[Category: Horse liver e enzyme]]
-[[Category: Nad]]
-[[Category: Oxidoreductase]]
-[[Category: Pentafluorobenzyl alcohol]]
-[[Category: Phe93 to trp substitution]]

6owm

From Proteopedia

Current revision

Horse liver F93W alcohol dehydrogenase complexed with NAD and pentafluorobenzyl alcohol

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox