2H5D

0.9A resolution crystal structure of alpha-lytic protease complexed with a transition state analogue, MeOSuc-Ala-Ala-Pro-Val boronic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.9 Å
  • R-Value Free: 0.091 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Subangstrom crystallography reveals that short ionic hydrogen bonds, and not a His-Asp low-barrier hydrogen bond, stabilize the transition state in serine protease catalysis

Fuhrmann, C.N.Daugherty, M.D.Agard, D.A.

(2006) J.Am.Chem.Soc. 128: 9086-9102

  • DOI: 10.1021/ja057721o
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • To address questions regarding the mechanism of serine protease catalysis, we have solved two X-ray crystal structures of alpha-lytic protease (alphaLP) that mimic aspects of the transition states: alphaLP at pH 5 (0.82 A resolution) and alphaLP boun ...

    To address questions regarding the mechanism of serine protease catalysis, we have solved two X-ray crystal structures of alpha-lytic protease (alphaLP) that mimic aspects of the transition states: alphaLP at pH 5 (0.82 A resolution) and alphaLP bound to the peptidyl boronic acid inhibitor, MeOSuc-Ala-Ala-Pro-boroVal (0.90 A resolution). Based on these structures, there is no evidence of, or requirement for, histidine-flipping during the acylation step of the reaction. Rather, our data suggests that upon protonation of His57, Ser195 undergoes a conformational change that destabilizes the His57-Ser195 hydrogen bond, preventing the back-reaction. In both structures the His57-Asp102 hydrogen bond in the catalytic triad is a normal ionic hydrogen bond, and not a low-barrier hydrogen bond (LBHB) as previously hypothesized. We propose that the enzyme has evolved a network of relatively short hydrogen bonds that collectively stabilize the transition states. In particular, a short ionic hydrogen bond (SIHB) between His57 Nepsilon2 and the substrate's leaving group may promote forward progression of the TI1-to-acylenzyme reaction. We provide experimental evidence that refutes use of either a short donor-acceptor distance or a downfield 1H chemical shift as sole indicators of a LBHB.


    Related Citations: 
    • 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
    • The 0.83A resolution crystal structure of alpha-lytic protease reveals the detailed structure of the active site and identifies a source of conformational strain
      Fuhrmann, C.N.,Kelch, B.A.,Ota, N.,Agard, D.A.
      (2004) J.Mol.Biol. 338: 999


    Organizational Affiliation

    Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94143-2240, 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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MEOSUC-ALA-ALA-PRO-ALA BORONIC ACID INHIBITOR
B
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000316
Query on PRD_000316
BMETHOXYSUCCINYL-ALA-ALA-PRO-VALINE BORONIC ACIDPeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.9 Å
  • R-Value Free: 0.091 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 65.768α = 90.00
b = 65.768β = 90.00
c = 79.554γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
startingmodel building
SHELXL-97refinement
SCALEPACKdata scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-09-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Type: Other