6M9F

PSEUDOMONAS SERINE-CARBOXYL PROTEINASE (SEDOLISIN) COMPLEXED WITH THE INHIBITOR Tyrostatin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.219 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Inhibitor complexes of the Pseudomonas serine-carboxyl proteinase

Wlodawer, A.Li, M.Gustchina, A.Dauter, Z.Uchida, K.Oyama, H.Goldfarb, N.E.Dunn, B.M.Oda, K.

(2001) Biochemistry 40: 15602-15611

  • DOI: 10.1021/bi011817n
  • Primary Citation of Related Structures:  
    6M8W, 6M8Y, 6M9C, 6M9D, 6M9F

  • PubMed Abstract: 
  • Crystal structures of the serine-carboxyl proteinase from Pseudomonas sp. 101 (PSCP), complexed with a number of inhibitors, have been solved and refined at high- to atomic-level resolution. All of these inhibitors (tyrostatin, pseudo-tyrostatin, AcIPF, AcIAF, and chymostatin, as well as previously studied iodotyrostatin and pseudo-iodotyrostatin) make covalent bonds to the active site Ser287 through their aldehyde moieties, while their side chains occupy subsites S1-S4 of the enzyme ...

    Crystal structures of the serine-carboxyl proteinase from Pseudomonas sp. 101 (PSCP), complexed with a number of inhibitors, have been solved and refined at high- to atomic-level resolution. All of these inhibitors (tyrostatin, pseudo-tyrostatin, AcIPF, AcIAF, and chymostatin, as well as previously studied iodotyrostatin and pseudo-iodotyrostatin) make covalent bonds to the active site Ser287 through their aldehyde moieties, while their side chains occupy subsites S1-S4 of the enzyme. The mode of binding of the inhibitors is almost identical for their P1 and P2 side chains, while significant differences are observed for P3 and P4 (if present). Kinetic parameters for the binding of these nanomolar inhibitors to PSCP have been established and correlated with the observed mode of binding. The preferences of this enzyme for a larger side chain in P2 as well as Tyr or Phe in P1 are explained by the size, shape, and characteristics of the S2 and S1 regions of the protein structure, respectively. Networks of hydrogen bonds involving glutamic and aspartic acids have been analyzed for the atomic-resolution structure of the native enzyme. PSCP contains a calcium-binding site that consists of Asp328, Asp348, three amide carbonyl groups, and a water molecule, in almost perfect octahedral coordination. The presence of Ca(2+) cation is necessary for the activity of the enzyme.


    Organizational Affiliation

    Protein Structure Section, Macromolecular Crystallography Laboratory, and Intramural Research Support Program, SAIC Frederick, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA. wlodawer@ncifcrf.gov



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SEDOLISINA368Pseudomonas sp. 101Mutation(s): 0 
Gene Names: pcp
EC: 3.4.21.100
UniProt
Find proteins for P42790 (Pseudomonas sp. (strain 101))
Explore P42790 
Go to UniProtKB:  P42790
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TyrostatinB4KitasatosporaMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYE
Query on TYE
BL-PEPTIDE LINKINGC9 H13 N O2TYR
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002328
Query on PRD_002328
BTYROSTATIN (Bound Form)Peptide-like / Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.219 
  • R-Value Observed: 0.193 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.24α = 90
b = 98.24β = 90
c = 83.39γ = 120
Software Package:
Software NamePurpose
SHELXLrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan13460043
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK18865 & AI28571
National Institutes of Health/National Cancer Institute (NIH/NCI)United Statesintramural funds

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Author supporting evidence