spacer
spacer

PDBsum entry 1qlh

Go to PDB code: 
protein ligands metals links
Oxidoreductase PDB id
1qlh
Jmol
Contents
Protein chain
374 a.a. *
Ligands
NAD
Metals
_ZN ×2
Waters ×88
* Residue conservation analysis
PDB id:
1qlh
Name: Oxidoreductase
Title: Horse liver alcohol dehydrogenase complexed to NAD double mutant of gly 293 ala and pro 295 thr
Structure: Alcohol dehydrogenase. Chain: a. Synonym: adh, alcohol dehydrogenase e chain. Engineered: yes. Mutation: yes
Source: Equus caballus. Horse. Organism_taxid: 9796. Organ: liver. Cellular_location: cytoplasm. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: e.Coli expressed mutant protein
Biol. unit: Dimer (from PDB file)
Resolution:
2.07Å     R-factor:   0.209     R-free:   0.254
Authors: S.Ramaswamy,B.V.Plapp
Key ref:
S.Ramaswamy et al. (1999). Substitutions in a flexible loop of horse liver alcohol dehydrogenase hinder the conformational change and unmask hydrogen transfer. Biochemistry, 38, 13951-13959. PubMed id: 10529241 DOI: 10.1021/bi991731i
Date:
31-Aug-99     Release date:   02-Jan-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00327  (ADH1E_HORSE) -  Alcohol dehydrogenase E chain
Seq:
Struc:
375 a.a.
374 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.1.1.1.1  - Alcohol dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. An alcohol + NAD+ = an aldehyde or ketone + NADH
2. A secondary alcohol + NAD+ = a ketone + NADH
alcohol
+
NAD(+)
Bound ligand (Het Group name = NAD)
matches with 97.00% similarity
= aldehyde or ketone
+ NADH
secondary alcohol
+ NAD(+)
= ketone
+ NADH
      Cofactor: Zn(2+) or Fe cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     oxidoreductase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi991731i Biochemistry 38:13951-13959 (1999)
PubMed id: 10529241  
 
 
Substitutions in a flexible loop of horse liver alcohol dehydrogenase hinder the conformational change and unmask hydrogen transfer.
S.Ramaswamy, D.H.Park, B.V.Plapp.
 
  ABSTRACT  
 
When horse liver alcohol dehydrogenase binds coenzyme, a rotation of about 10 degrees brings the catalytic domain closer to the coenzyme binding domain and closes the active site cleft. The conformational change requires that a flexible loop containing residues 293-298 in the coenzyme binding domain rearranges so that the coenzyme and some amino acid residues from the catalytic domain can be accommodated. The change appears to control the rate of dissociation of the coenzyme and to be necessary for installation of the proton relay system. In this study, directed mutagenesis produced the activated Gly293Ala/Pro295Thr enzyme. X-ray crystallography shows that the conformations of both free and complexed forms of the mutated enzyme and wild-type apoenzyme are very similar. Binding of NAD(+) and 2,2, 2-trifluoroethanol do not cause the conformational change, but the nicotinamide ribose moiety and alcohol are not in a fixed position. Although the Gly293Ala and Pro295Thr substitutions do not disturb the apoenzyme structure, molecular modeling shows that the new side chains cannot be accommodated in the closed native holoenzyme complex without steric alterations. The mutated enzyme may be active in the "open" conformation. The turnover numbers with ethanol and acetaldehyde increase 1.5- and 5.5-fold, respectively, and dissociation constants for coenzymes and other kinetic constants increase 40-2,000-fold compared to those of the native enzyme. Substrate deuterium isotope effects on the steady state V or V/K(m) parameters of 4-6 with ethanol or benzyl alcohol indicate that hydrogen transfer is a major rate-limiting step in catalysis. Steady state oxidation of benzyl alcohol is most rapid above a pK of about 9 for V and V/K(m) and is 2-fold faster in D(2)O than in H(2)O. The results are consistent with hydride transfer from a ground state zinc alkoxide that forms a low-barrier hydrogen bond with the hydroxyl group of Ser48.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20000378 B.S.Avvaru, C.U.Kim, K.H.Sippel, S.M.Gruner, M.Agbandje-McKenna, D.N.Silverman, and R.McKenna (2010).
A short, strong hydrogen bond in the active site of human carbonic anhydrase II.
  Biochemistry, 49, 249-251.
PDB code: 3ks3
19583966 B.V.Plapp (2010).
Conformational changes and catalysis by alcohol dehydrogenase.
  Arch Biochem Biophys, 493, 3.  
19857201 M.Klimacek, and B.Nidetzky (2010).
The oxyanion hole of Pseudomonas fluorescens mannitol 2-dehydrogenase: a novel structural motif for electrostatic stabilization in alcohol dehydrogenase active sites.
  Biochem J, 425, 455-463.  
20441762 S.Hayward, and A.Kitao (2010).
The effect of end constraints on protein loop kinematics.
  Biophys J, 98, 1976-1985.  
19022233 S.Pal, D.H.Park, and B.V.Plapp (2009).
Activity of yeast alcohol dehydrogenases on benzyl alcohols and benzaldehydes: characterization of ADH1 from Saccharomyces carlsbergensis and transition state analysis.
  Chem Biol Interact, 178, 16-23.  
18362150 J.Pavlicek, S.L.Coon, S.Ganguly, J.L.Weller, S.A.Hassan, D.L.Sackett, and D.C.Klein (2008).
Evidence that proline focuses movement of the floppy loop of arylalkylamine N-acetyltransferase (EC 2.3.1.87).
  J Biol Chem, 283, 14552-14558.  
19484137 G.Parkin (2007).
Applications of Tripodal [S(3)] and [Se(3)] L(2)X Donor Ligands to Zinc, Cadmium and Mercury Chemistry: Organometallic and Bioinorganic Perspectives.
  New J Chem, 31, 1996-2014.  
16756501 S.Hammes-Schiffer, and S.J.Benkovic (2006).
Relating protein motion to catalysis.
  Annu Rev Biochem, 75, 519-541.  
16714351 S.Hayward, and A.Kitao (2006).
Molecular dynamics simulations of NAD+-induced domain closure in horse liver alcohol dehydrogenase.
  Biophys J, 91, 1823-1831.  
  16511145 J.Esclapez, K.L.Britton, P.J.Baker, M.Fisher, C.Pire, J.Ferrer, M.J.Bonete, and D.W.Rice (2005).
Crystallization and preliminary X-ray analysis of binary and ternary complexes of Haloferax mediterranei glucose dehydrogenase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 743-746.  
14661950 L.Esposito, I.Bruno, F.Sica, C.A.Raia, A.Giordano, M.Rossi, L.Mazzarella, and A.Zagari (2003).
Crystal structure of a ternary complex of the alcohol dehydrogenase from Sulfolobus solfataricus.
  Biochemistry, 42, 14397-14407.
PDB code: 1r37
12632471 M.Elstner, Q.Cui, P.Munih, E.Kaxiras, T.Frauenheim, and M.Karplus (2003).
Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: applications to structural and energetic analysis.
  J Comput Chem, 24, 565-581.  
12855684 T.H.Venkataramaiah, and B.V.Plapp (2003).
Formamides mimic aldehydes and inhibit liver alcohol dehydrogenases and ethanol metabolism.
  J Biol Chem, 278, 36699-36706.
PDB code: 1p1r
12491384 H.C.Lo, and R.H.Fish (2002).
Biomimetic NAD(+) models for tandem cofactor regeneration, horse liver alcohol dehydrogenase recognition of 1,4-NADH derivatives, and chiral synthesis.
  Angew Chem Int Ed Engl, 41, 478-481.  
12146981 M.Klimacek, and B.Nidetzky (2002).
Examining the relative timing of hydrogen abstraction steps during NAD(+)-dependent oxidation of secondary alcohols catalyzed by long-chain D-mannitol dehydrogenase from Pseudomonas fluorescens using pH and kinetic isotope effects.
  Biochemistry, 41, 10158-10165.  
11306065 A.Allali-Hassani, B.Crosas, X.Parés, and J.Farrés (2001).
Kinetic effects of a single-amino acid mutation in a highly variable loop (residues 114-120) of class IV ADH.
  Chem Biol Interact, 130, 435-444.  
11274460 M.S.Niederhut, B.J.Gibbons, S.Perez-Miller, and T.D.Hurley (2001).
Three-dimensional structures of the three human class I alcohol dehydrogenases.
  Protein Sci, 10, 697-706.
PDB codes: 1hso 1hsz 1ht0
10969022 D.B.Northrop, and Y.K.Cho (2000).
Effects of high pressure on solvent isotope effects of yeast alcohol dehydrogenase.
  Biophys J, 79, 1621-1628.  
10801319 J.B.Thoden, T.M.Wohlers, J.L.Fridovich-Keil, and H.M.Holden (2000).
Crystallographic evidence for Tyr 157 functioning as the active site base in human UDP-galactose 4-epimerase.
  Biochemistry, 39, 5691-5701.
PDB codes: 1ek5 1ek6
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.