1QF0

THERMOLYSIN (E.C.3.4.24.27) COMPLEXED WITH (2-SULPHANYL-3-PHENYLPROPANOYL)-PHE-TYR. PARAMETERS FOR ZN-BIDENTATION OF MERCAPTOACYLDIPEPTIDES IN METALLOENDOPEPTIDASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of alpha-mercaptoacyldipeptides in the thermolysin active site: structural parameters for a Zn monodentation or bidentation in metalloendopeptidases.

Gaucher, J.F.Selkti, M.Tiraboschi, G.Prange, T.Roques, B.P.Tomas, A.Fournie-Zaluski, M.C.

(1999) Biochemistry 38: 12569-12576

  • Primary Citation of Related Structures:  1QF1, 1QF2

  • PubMed Abstract: 
  • Three alpha-mercaptoacyldipeptides differing essentially in the size of their C-terminal residues have been crystallized in the thermolysin active site. A new mode of binding was observed for 3 [HS-CH(CH(2)Ph)CO-Phe-Tyr] and 4 [HS-CH((CH(2))(4)CH(3)) ...

    Three alpha-mercaptoacyldipeptides differing essentially in the size of their C-terminal residues have been crystallized in the thermolysin active site. A new mode of binding was observed for 3 [HS-CH(CH(2)Ph)CO-Phe-Tyr] and 4 [HS-CH((CH(2))(4)CH(3))CO-Phe-Ala], in which the mercaptoacyl moieties act as bidentates with Zn-S and Zn-O distances of 2.3 and 2.4 A, respectively, the side chains fitting the S(1), S(1)', and S(2)' pockets. Moreover, a distance of 3.1 A between the sulfur atom and the OE1 of Glu(143) suggests that they are H-bonded and that one of these atoms is protonated. This H-bond network involving Glu(143), the mercaptoacyl group of the inhibitor, and the Zn ion could be considered a "modified" transition state mimic of the peptide bond hydrolysis. Due to the presence of the hindering (5-phenyl)proline, the inhibitor HS-CH(CH(2)Ph)CO-Gly-(5-Ph)Pro (2) interacts through the usual Zn monodentation via the thiol group and occupancy of S(1)' and S(2)' subsites by the aromatic moieties, the proline ring being outside the active site. The inhibitory potencies are consistent with these structural data, with higher affinities for 3 (4.2 x 10(-)(8) M) and 4 (4.8 x 10(-)(8) M) than for 2 (1.2 x 10(-)(6) M). The extension of the results, obtained with thermolysin being considered as the model of physiological zinc metallopeptidases, allows inhibitor-recognition modes for other peptidases, such as angiotensin converting enzyme and neutral endopeptidase, to be proposed and opens interesting possibilities for the design of new classes of inhibitors.


    Related Citations: 
    • Design of Orally Active Dual Inhibitors of Neutral Endopeptidase and Angiotensin-Converting Enzyme with Long Duration of Action
      Fournie-Zaluski, M.-C.,Coric, P.,Thery, V.,Gonzalez, W.,Meudal, H.,Turcaud, S.,Michel, J.- B.,Roques, B.
      (1996) J.Med.Chem. 39: 2594
    • A Structural Analysis of Metal Substitutions in the Active Site of Thermolysin
      Holland, D.R.,Hausrath, A.C.,Juers, D.,Matthews, B.W.
      (1995) Protein Sci. 4: 1955
    • Three Dimensional Structure of Thermolysin
      Matthews, B.W.,Jansonius, J.N.,Colman, P.M.,Schoenborn, B.P.,Dupourque, D.
      (1972) Nature New Biol. 238: 37
    • Optimal Recognition of Neutral Endopeptidase and Angiotensine-Converting Enzyme Active Sites by Mercaptoacyldipeptides as a Means to Design Potent Dual Inhibitors
      Coric, P.,Turcaud, S.,Meudal, H.,Roques, B.P.,Fournie-Zaluski, M.-C.
      (1996) J.Med.Chem. 39: 1210


    Organizational Affiliation

    Laboratoire de Cristallographie & RMN Biologiques, CNRS EP 2075, UFR des Sciences Pharmaceutiques et Biologiques, 4 Avenue de l'Observatoire, 75270 Paris Cedex 06, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (THERMOLYSIN)
A
316Bacillus thermoproteolyticusGene Names: npr
EC: 3.4.24.27
Find proteins for P00800 (Bacillus thermoproteolyticus)
Go to UniProtKB:  P00800
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
TI2
Query on TI2

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Download CCD File 
A
(2-SULFANYL-3-PHENYLPROPANOYL)-PHE-TYR
C27 H28 N2 O5 S
GIVBBFGMRNXKPE-HJOGWXRNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TI2Ki: 42 nM BINDINGMOAD
TI2Ki: 42 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.161 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.370α = 90.00
b = 93.370β = 90.00
c = 131.790γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
CCP4data scaling
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-12-29
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance