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


Ligand Structure Quality Assessment 


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:  
    1D1S, 1D1T

  • 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)  |  3D 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40394
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],
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],
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



Ligand Structure Quality Assessment 


View more in-depth experimental data
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