1TAL

ALPHA-LYTIC PROTEASE AT 120 K (SINGLE STRUCTURE MODEL)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Conformational substates in enzyme mechanism: the 120 K structure of alpha-lytic protease at 1.5 A resolution.

Rader, S.D.Agard, D.A.

(1997) Protein Sci. 6: 1375-1386

  • DOI: 10.1002/pro.5560060701
  • Primary Citation of Related Structures:  
  • Also Cited By: 3M7U, 3M7T

  • PubMed Abstract: 
  • Insight into the dynamic properties of alpha-lytic protease (alpha LP) has been obtained through the use of low-temperature X-ray crystallography and multiple-conformation refinement. Previous studies of alpha LP have shown that the residues around t ...

    Insight into the dynamic properties of alpha-lytic protease (alpha LP) has been obtained through the use of low-temperature X-ray crystallography and multiple-conformation refinement. Previous studies of alpha LP have shown that the residues around the active site are able to move significantly to accommodate substrates of different sizes. Here we show a link between the ability to accommodate ligands and the dynamics of the binding pocket. Although the structure of alpha LP at 120 K has B-factors with a uniformly low value of 4.8 A2 for the main chain, four regions stand out as having significantly higher B-factors. Because thermal motion should be suppressed at cryogenic temperatures, the high B-factors are interpreted as the result of trapped conformational substates. The active site residues that are perturbed during accommodation of different substrates are precisely those showing conformational substates, implying that substrate binding selects a subset of conformations from the ensemble of accessible states. To better characterize the precise nature of these substates, a protein model consisting of 16 structures has been refined and evaluated. The model reveals a number of features that could not be well-described by conventional B-factors: for example, 40% of the main-chain residue conformations are distributed asymmetrically or in discrete clusters. Furthermore, these data demonstrate an unexpected correlation between motions on either side of the binding pocket that we suggest is a consequence of "dynamic close packing." These results provide strong evidence for the role of protein dynamics in substrate binding and are consistent with the results of dynamic studies of ligand binding in myoglobin and ribonuclease A.


    Related Citations: 
    • Structural Basis for Broad Specificity in Alpha-Lytic Protease
      Bone, R.,Fujishige, A.,Kettner, C.A.,Agard, D.A.
      (1991) Biochemistry 30: 10388
    • Serine Protease Mechanism: Structure of an Inhibitory Complex of Alpha-Lytic Protease and a Tightly Bound Peptide Boronic Acid
      Bone, R.,Shenvi, A.B.,Kettner, C.A.,Agard, D.A.
      (1987) Biochemistry 26: 7609
    • Refined Structure of Alpha-Lytic Protease at 1.7 A Resolution. Analysis of Hydrogen Bonding and Solvent Structure
      Fujinaga, M.,Delbaere, L.T.,Brayer, G.D.,James, M.N.
      (1985) J.Mol.Biol. 184: 479
    • Structural Analysis of Specificity: Alpha-Lytic Protease Complexes with Analogues of Reaction Intermediates
      Bone, R.,Frank, D.,Kettner, C.A.,Agard, D.A.
      (1989) Biochemistry 28: 7600
    • Structural Plasticity Broadens the Specificity of an Engineered Protease
      Bone, R.,Silen, J.L.,Agard, D.A.
      (1989) Nature 339: 191
    • Molecular Structure of the Alpha-Lytic Protease from Myxobacter 495 at 2.8 Angstroms Resolution
      Brayer, G.D.,Delbaere, L.T.,James, M.N.
      (1979) J.Mol.Biol. 131: 743


    Organizational Affiliation

    Graduate Group in Biophysics, University of California at San Francisco 94143-0448, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA-LYTIC PROTEASE
A
198Lysobacter enzymogenesMutation(s): 0 
Gene Names: alpha-LP
EC: 3.4.21.12
Find proteins for P00778 (Lysobacter enzymogenes)
Go to UniProtKB:  P00778
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
TAM
Query on TAM

Download SDF File 
Download CCD File 
A
TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.165 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 65.800α = 90.00
b = 65.800β = 90.00
c = 79.500γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORphasing
DENZOdata reduction
X-PLORrefinement
X-PLORmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-04-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance