1D1S

WILD-TYPE HUMAN SIGMA (CLASS IV) ALCOHOL DEHYDROGENASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Methionine-141 directly influences the binding of 4-methylpyrazole in human sigma sigma alcohol dehydrogenase.

Xie, P.T.Hurley, T.D.

(1999) Protein Sci 8: 2639-2644

  • DOI: 10.1110/ps.8.12.2639
  • Primary Citation of Related Structures:  
    1D1T, 1D1S

  • PubMed Abstract: 
  • Pyrazole and its 4-alkyl substituted derivatives are potent inhibitors for many alcohol dehydrogenases. However, the human sigma sigma isoenzyme exhibits a 580-fold lower affinity for 4-methylpyrazole than does the human beta1beta1 isoenzyme, with which it shares 69% sequence identity ...

    Pyrazole and its 4-alkyl substituted derivatives are potent inhibitors for many alcohol dehydrogenases. However, the human sigma sigma isoenzyme exhibits a 580-fold lower affinity for 4-methylpyrazole than does the human beta1beta1 isoenzyme, with which it shares 69% sequence identity. In this study, structural and kinetic studies were utilized in an effort to identify key structural features that affect the binding of 4-methylpyrazole in human alcohol dehydrogenase isoenzymes. We have extended the resolution of the human sigma sigma alcohol dehydrogenase (ADH) isoenzyme to 2.5 A resolution. Comparison of this structure to the human beta1beta1 isoenzyme structure indicated that the side-chain position for Met141 in sigma sigma ADH might interfere with 4-methylpyrazole binding. Mutation of Met141 in sigma sigma ADH to Leu (sigma141L) lowers the Ki for 4-methylpyrazole from 350 to 10 microM, while having a much smaller effect on the Ki for pyrazole. Thus, the mutagenesis results show that the residue at position 141, which lines the substrate-binding pocket at a position close to the methyl group of 4-methylpyrazole, directly affects the binding of the inhibitor. To rule out nonspecific structural changes due to the mutation, the X-ray structure of the sigma141L mutant enzyme was determined to 2.4 A resolution. The three-dimensional structure of the mutant enzyme is identical to the wild-type enzyme, with the exception of the residue at position 141. Thus, the differences in 4-methylpyrazole binding between the mutant and wild-type sigma sigma ADH isoenzymes can be completely ascribed to the local changes in the topology of the substrate binding site, and provides an explanation for the class-specific differences in 4-methylpyrazole binding to the human ADH isoenzymes.


    Related Citations: 
    • X-ray structure of human class IV sigma-sigma alcohol dehydrogenase
      Xie, P.T., Parsons, S.H., Speckhard, D.C., Bosron, W.F., Hurley, T.D.
      (1997) J Biol Chem 272: 18558

    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis 46202-5122, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALCOHOL DEHYDROGENASE CLASS IV SIGMA CHAINA, B, C, D373Homo sapiensMutation(s): 0 
Gene Names: ADH7
EC: 1.1.1.1 (PDB Primary Data), 1.1.1.105 (UniProt), 1.1.1.66 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P40394 (Homo sapiens)
Explore P40394 
Go to UniProtKB:  P40394
PHAROS:  P40394
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
BA [auth B], HA [auth C], P [auth A], SA [auth D]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
CAC
Query on CAC

Download Ideal Coordinates CCD File 
AA [auth B], O [auth A], X [auth B], Y [auth B], Z [auth B]CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
CA [auth C] , DA [auth C] , E [auth A] , EA [auth C] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , 
CA [auth C],  DA [auth C],  E [auth A],  EA [auth C],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  IA [auth D],  J [auth A],  JA [auth D],  KA [auth D],  LA [auth D],  MA [auth D],  Q [auth B],  R [auth B],  S [auth B],  T [auth B],  U [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
FA [auth C] , GA [auth C] , K [auth A] , L [auth A] , M [auth A] , N [auth A] , NA [auth D] , OA [auth D] , 
FA [auth C],  GA [auth C],  K [auth A],  L [auth A],  M [auth A],  N [auth A],  NA [auth D],  OA [auth D],  PA [auth D],  QA [auth D],  RA [auth D],  V [auth B],  W [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.4α = 90
b = 90.9β = 99.6
c = 121.1γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-09-29
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Data collection