1ADB

CRYSTALLOGRAPHIC STUDIES OF ISOSTERIC NAD ANALOGUES BOUND TO ALCOHOL DEHYDROGENASE: SPECIFICITY AND SUBSTRATE BINDING IN TWO TERNARY COMPLEXES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystallographic studies of isosteric NAD analogues bound to alcohol dehydrogenase: specificity and substrate binding in two ternary complexes.

Li, H.Hallows, W.H.Punzi, J.S.Pankiewicz, K.W.Watanabe, K.A.Goldstein, B.M.

(1994) Biochemistry 33: 11734-11744

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • CNAD (5-beta-D-ribofuranosylnicotinamide adenine dinucleotide) is an isosteric C-glycosidic analogue of NAD(H) containing a neutral pyridine ring. CPAD (5-beta-D-ribofuranosylpicolinamide adenine dinucleotide) is a closely related pyridine-containing ...

    CNAD (5-beta-D-ribofuranosylnicotinamide adenine dinucleotide) is an isosteric C-glycosidic analogue of NAD(H) containing a neutral pyridine ring. CPAD (5-beta-D-ribofuranosylpicolinamide adenine dinucleotide) is a closely related pyridine-containing analogue with the pyridine nitrogen on the opposite side of the ring. CNAD is a potent and specific inhibitor of horse liver alcohol dehydrogenase (LADH), binding with a dissociation constant in the nanomolar range. CPAD binds LADH with an affinity comparable to that of NAD. Crystal structures of CNAD and CPAD bound to LADH are presented at 2.4 and 2.7 A, respectively. The two complexes are isomorphous, crystallizing in the triclinic system with cell dimensions different from those seen in previous ternary LADH complexes. Structures were solved using the molecular replacement method and refined to crystallographic R values of 18% (CNAD) and 17% (CPAD). Both inhibitors bind to the "closed" form of LADH in the normal cofactor-binding cleft. The conformation of LADH-bound CPAD closely mimics that of LADH-bound NAD(H). The data suggest that alcohol substrate binds directly to the catalytic zinc atom. In the CNAD complex, the pyridine nitrogen replaces alcohol as the fourth coordination ligand to the active site zinc atom, while all other polar interactions remain the same as those of bound NAD(H). The zinc-nitrogen ligand explains the high affinity of CNAD for LADH.


    Related Citations: 
    • Three-Dimensional Structure of Isonicotinimidylated Liver Alcohol Dehydrogenase
      Plapp, B.V.,Eklund, H.,Jones, T.A.,Branden, C.-I.
      (1983) J.Biol.Chem. 258: 5537
    • Structural Comparisons of Mammalian, Yeast and Bacillar Alcohol Dehydrogenases
      Eklund, H.,Branden, C.-I.,Jornvall, H.
      (1976) J.Mol.Biol. 102: 61
    • Structural and Functional Similarities within the Coenzyme Binding Domains of Dehydrogenases
      Ohlsson, I.,Nordstrom, B.,Branden, C.-I.
      (1974) J.Mol.Biol. 89: 339
    • Three-Dimensional Structure of Horse Liver Alcohol Dehydrogenase at 2.4 Angstroms Resolution
      Eklund, H.,Nordstrom, B.,Zeppezauer, E.,Soderlund, G.,Ohlsson, I.,Boiwe, T.,Soderberg, B.-O.,Tapia, O.,Branden, C.-I.,Akeson, A.
      (1976) J.Mol.Biol. 102: 27
    • The Binding of Nucleotides to Horse Liver Alcohol Dehydrogenase
      Nordstrom, B.,Branden, C.-I.
      (1975) STRUCTURE AND CONFORMATION OF NUCLEIC ACIDS AND PROTEIN-NUCLEIC ACID INTERACTIONS : PROCEEDINGS OF THE FOURTH ANNUAL HARRY STEENBOCK SYMPOSIUM, JUNE 16-19, 1974, MADISON, WISCONSIN --: 387
    • Structural Differences between Apo-and Holoenzyme of Horse Liver Alcohol Dehydrogenase
      Eklund, H.,Branden, C.-I.
      (1979) J.Biol.Chem. 254: 3458
    • Structure of Liver Alcohol Dehydrogenase at 2.9-Angstrom Resolution
      Branden, C.-I.,Eklund, H.,Nordstrom, B.,Boiwe, T.,Soderlund, G.,Zeppezauer, E.,Ohlsson, I.,Akeson, A.
      (1973) Proc.Natl.Acad.Sci.USA 70: 2439
    • The Conformation of Adenosine Diphosphoribose and 8-Bromoadenosine Diphosphoribose When Bound to Liver Alcohol Dehydrogenase
      Abdallah, M.A.,Biellmann, J.-F.,Nordstrom, B.,Branden, C.-I.
      (1975) Eur.J.Biochem. 50: 475
    • X-Ray Studies of the Binding of Cibacron Blue F3Ga to Liver Alcohol Dehydrogenase
      Biellmann, J.-F.,Samama, J.-P.,Branden, C.I.,Eklund, H.
      (1979) Eur.J.Biochem. 102: 107
    • Alcohol Dehydrogenases
      Branden, C.-I.,Jornvall, H.,Eklund, H.,Furugren, B.
      (1975) The Enzymes,Third Edition 11: 103
    • Crystal Structures of the Active Site in Specifically Metal-Depleted and Cobalt-Substituted Horse Liver Alcohol Dehydrogenase Derivatives
      Schneider, G.,Eklund, H.,Cedergren-Zeppezauer, E.,Zeppezauer, M.
      (1983) Proc.Natl.Acad.Sci.USA 80: 5289
    • Crystallographic Investigations of Nicotinamide Adenine Dinucleotide Binding to Horse Liver Alcohol Dehydrogenase
      Eklund, H.,Samama, J.-P.,Jones, T.A.
      (1984) Biochemistry 23: 5982
    • Interdomain Motion in Liver Alcohol Dehydrogenase. Structural and Energetic Analysis of the Hinge Bending Mode
      Colonna-Cesari, F.,Perahia, D.,Karplus, M.,Eklund, H.,Branden, C.I.,Tapia, O.
      (1986) J.Biol.Chem. 261: 15273
    • Crystal-Structure Determination of Reduced Nicotinamide Adenine Dinucleotide Complex with Horse Liver Alcohol Dehydrogenase Maintained in its Apo Conformation by Zinc-Bound Imidazole
      Cedergren-Zeppezauer, E.
      (1983) Biochemistry 22: 5761
    • X-Ray Investigation of the Binding of 1,10-Phenanthroline and Imidazole to Horse-Liver Alcohol Dehydrogenase
      Boiwe, T.,Branden, C.-I.
      (1977) Eur.J.Biochem. 77: 173
    • The Crystal Structure of Complexes between Horse Liver Alcohol Dehydrogenase and the Coenzyme Analogues 3-Iodopyridine-Adenine Dinucleotide and Pyridine-Adenine Dinucleotide
      Samama, J.-P.,Zeppezauer, E.,Biellmann, J.-F.,Branden, C.-I.
      (1977) Eur.J.Biochem. 81: 403
    • Structure of Horse Liver Alcohol Dehydrogenase. I. Structural Symmetry and Conformational Changes
      Branden, C.-I.
      (1965) Arch.Biochem.Biophys. 112: 215
    • Subunit Conformation of Yeast Alcohol Dehydrogenase
      Jornvall, H.,Eklund, H.,Branden, C.-I.
      (1978) J.Biol.Chem. 253: 8414
    • Crystal Structure Determinations of Coenzyme Analogue and Substrate Complexes of Liver Alcohol Dehydrogenase. Binding of 1,4,5,6-Tetrahydronicotinamide Adenine Dinucleotide and Trans-4-(N,N-Dimethylamino)Cinnamaldehyde to the Enzyme
      Cedergren-Zeppezauer, E.,Samama, J.-P.,Eklund, H.
      (1982) Biochemistry 21: 4895
    • Crystallography of Liver Alcohol Dehydrogenase Complexed with Substrates
      Plapp, B.V.,Eklund, H.,Branden, C.-I.
      (1978) J.Mol.Biol. 122: 23
    • 5-Methylnicotinamide-Adenine Dinucleotide. Kinetic Investigation with Major and Minor Isoenzymes of Liver Alcohol Dehydrogenase and Structural Determination of its Binary Complex with Alcohol Dehydrogenase
      Samama, J.-P.,Wrixon, A.D.,Biellmann, J.-F.
      (1981) Eur.J.Biochem. 118: 479
    • Binding of Substrate in a Ternary Complex of Horse Liver Alcohol Dehydrogenase
      Eklund, H.,Plapp, B.V.,Samama, J.-P.,Branden, C.-I.
      (1982) J.Biol.Chem. 257: 14349
    • Pyrazole Binding in Crystalline Binary and Ternary Complexes with Liver Alcohol Dehydrogenase
      Eklund, H.,Samama, J.-P.,Wallen, L.
      (1982) Biochemistry 21: 4858
    • Binding of Salicylate in the Adenosine-Binding Pocket of Dehydrogenases
      Einarsson, R.,Eklund, H.,Zeppezauer, E.,Boiwe, T.,Branden, C.-I.
      (1974) Eur.J.Biochem. 49: 41
    • Crystallization of Liver Alcohol Dehydrogenase Activated by the Modification of Amino Groups
      Plapp, B.V.,Zeppezauer, E.,Branden, C.-I.
      (1978) J.Mol.Biol. 119: 451
    • The Structure of Horse Liver Alcohol Dehydrogenase
      Eklund, H.,Nordstrom, B.,Zeppezauer, E.,Soderlund, G.,Ohlsson, I.,Boiwe, T.,Branden, C.-I.
      (1974) FEBS Lett. 44: 200


    Organizational Affiliation

    Department of Biophysics, University of Rochester Medical Center, New York 14642.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALCOHOL DEHYDROGENASE
A, B
374Equus caballusMutation(s): 0 
EC: 1.1.1.1
Find proteins for P00327 (Equus caballus)
Go to UniProtKB:  P00327
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EOH
Query on EOH

Download SDF File 
Download CCD File 
A, B
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
CND
Query on CND

Download SDF File 
Download CCD File 
A, B
5-BETA-D-RIBOFURANOSYLNICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H27 N7 O14 P2
UINNILASBHZOTM-KMXXXSRASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.180 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 52.100α = 103.30
b = 44.700β = 87.90
c = 93.500γ = 70.40
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-06-03
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other