5ADH

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 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:  
    5ADH, 8ADH

  • 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: 
    • Crystallographic Investigations of Nicotinamide Adenine Dinucleotide Binding to Horse Liver Alcohol Dehydrogenase
      Eklund, H., Samama, J.-P., Jones, T.A.
      (1984) Biochemistry 23: 5982
    • 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 U S A 80: 5289
    • 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
    • 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
    • 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
    • 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
    • Pyrazole Binding in Crystalline Binary and Ternary Complexes with Liver Alcohol Dehydrogenase
      Eklund, H., Samama, J.-P., Wallen, L.
      (1982) Biochemistry 21: 4858
    • 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
    • 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
    • Structural Differences between Apo-and Holoenzyme of Horse Liver Alcohol Dehydrogenase
      Eklund, H., Branden, C.-I.
      (1979) J Biol Chem 254: 3458
    • 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
    • Crystallography of Liver Alcohol Dehydrogenase Complexed with Substrates
      Plapp, B.V., Eklund, H., Branden, C.-I.
      (1978) J Mol Biol 122: 23
    • 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
    • Subunit Conformation of Yeast Alcohol Dehydrogenase
      Jornvall, H., Eklund, H., Branden, C.-I.
      (1978) J Biol Chem 253: 8414
    • 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
    • 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
    • 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 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
    • Alcohol Dehydrogenases
      Branden, C.-I., Jornvall, H., Eklund, H., Furugren, B.
      (1975) The Enzymes,third Edition 11: 103
    • 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
    • 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 and Functional Similarities within the Coenzyme Binding Domains of Dehydrogenases
      Ohlsson, I., Nordstrom, B., Branden, C.-I.
      (1974) J Mol Biol 89: 339
    • 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
    • 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 U S A 70: 2439
    • Structure of Horse Liver Alcohol Dehydrogenase. I. Structural Symmetry and Conformational Changes
      Branden, C.-I.
      (1965) Arch Biochem Biophys 112: 215

    Organizational Affiliation

    *The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
APO-LIVER ALCOHOL DEHYDROGENASEA374Equus caballusMutation(s): 0 
EC: 1.1.1.1
Find proteins for P00327 (Equus caballus)
Explore P00327 
Go to UniProtKB:  P00327
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APR
Query on APR

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

Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56α = 90
b = 75.2β = 90
c = 181.7γ = 90

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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