5ADH

INTERDOMAIN MOTION IN LIVER ALCOHOL DEHYDROGENASE. STRUCTURAL AND ENERGETIC ANALYSIS OF THE HINGE BENDING MODE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Interdomain motion in liver alcohol dehydrogenase. Structural and energetic analysis of the hinge bending mode.

Colonna-Cesari, F.Perahia, D.Karplus, M.Eklund, H.Braden, C.I.Tapia, O.

(1986) J.Biol.Chem. 261: 15273-15280

  • Primary Citation of Related Structures:  
  • Also Cited By: 1HET

  • PubMed Abstract: 
  • A study of the hinge bending mode in the enzyme liver alcohol dehydrogenase is made by use of empirical energy functions. The enzyme is a dimer, with each monomer composed of a coenzyme binding domain and a catalytic domain with a large cleft between ...

    A study of the hinge bending mode in the enzyme liver alcohol dehydrogenase is made by use of empirical energy functions. The enzyme is a dimer, with each monomer composed of a coenzyme binding domain and a catalytic domain with a large cleft between the two. Superposition of the apoenzyme and holoenzyme crystal structures is used to determine a rigid rotation axis for closing of the cleft. It is shown that a rigid body transformation of the apoenzyme to the holoenzyme structure corresponds to a 10 degrees rotation of the catalytic domain about this axis. The rotation is not along the least-motion path for closing of the cleft but instead corresponds to the catalytic domain coming closer to the coenzyme binding domain by a sliding motion. Estimation of the energy associated with the interdomain motion of the apoenzyme over a range of 90 degrees (-40 to 50 degrees, where 0 degrees corresponds to the minimized crystal structure) demonstrates that local structural relaxation makes possible large-scale rotations with relatively small energy increments. A variety of structural rearrangements associated with the domain motion are characterized. They involve the hinge region residues that provide the covalent connections between the two domains and certain loop regions that are brought into contact by the rotation. Differences between the energy minimized and the holoenzyme structures point to the existence of alternative conformations for loops and to the importance of the ligands in the structural rearrangements.


    Related Citations: 
    • Crystallization of Liver Alcohol Denydrogenase Activated by the Modification of Amino Groups
      Plapp, B.V.,Zeppezauer, E.,Branden, C.-I.
      (1978) J.Mol.Biol. 119: 451
    • 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
    • Crystallography of Liver Alcohol Dehydrogenase Complexed with Substrates
      Plapp, B.V.,Eklund, H.,Branden, C.-I.
      (1978) J.Mol.Biol. 122: 23
    • 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
    • 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
    • Structural Differences between Apo-and Holoenzyme of Horse Liver Alcohol Dehydrogenase
      Eklund, H.,Branden, C.-I.
      (1979) J.Biol.Chem. 254: 3458
    • 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
    • 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
    • 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
    • Subunit Conformation of Yeast Alcohol Dehydrogenase
      Jornvall, H.,Eklund, H.,Branden, C.-I.
      (1978) J.Biol.Chem. 253: 8414
    • 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
    • Alcohol Dehydrogenases
      Branden, C.-I.,Jornvall, H.,Eklund, H.,Furugren, B.
      (1975) The Enzymes,Third Edition 11: 103
    • Structure of Horse Liver Alcohol Dehydrogenase. I. Structural Symmetry and Conformational Changes
      Branden, C.-I.
      (1965) Arch.Biochem.Biophys. 112: 215
    • 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
    • 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
    • Structural and Functional Similarities within the Coenzyme Binding Domains of Dehydrogenases
      Ohlsson, I.,Nordstrom, B.,Branden, C.-I.
      (1974) J.Mol.Biol. 89: 339
    • Crystal Structure Determinations of Coenzyme Analogue and Substrate Complexes of Liver Alcohol Dehydrogeanse. 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
    • 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
    • Structural Comparisons of Mammalian, Yeast and Bacillar Alcohol Dehydrogenases
      Eklund, H.,Branden, C.-I.,Jornvall, H.
      (1976) J.Mol.Biol. 102: 61
    • 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
    • Pyrazole Binding in Crystalline Binary and Ternary Complexes with Liver Alcohol Dehydrogenase
      Eklund, H.,Samama, J.-P.,Wallen, L.
      (1982) Biochemistry 21: 4858
    • 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
    • Structure of Liver Alcohol Dehydrogenase at 2.9-Angstroms 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
    • Structure of Triclinic Ternary Complex of Horse Liver Alcohol Dehydrogenase at 2.9 Angstroms Resolution
      Eklund, H.,Samama, J.-P.,Wallen, L.,Branden, C.-I.,Akeson, A.,Jones, T.A.
      (1981) J.Mol.Biol. 146: 561
    • Crystallographic Investigations of Nicotinamide Adenine Dinucleotide Binding to Horse Liver Alcohol Dehydrogenase
      Eklund, H.,Samama, J.-P.,Jones, T.A.
      (1984) Biochemistry 23: 5982



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
APO-LIVER ALCOHOL DEHYDROGENASE
A
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
APR
Query on APR

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Download CCD File 
A
ADENOSINE-5-DIPHOSPHORIBOSE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-KEOHHSTQSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

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Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 56.000α = 90.00
b = 75.200β = 90.00
c = 181.700γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1984-07-18
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Advisory, Derived calculations, Other