1A5I

CATALYTIC DOMAIN OF VAMPIRE BAT (DESMODUS ROTUNDUS) SALIVA PLASMINOGEN ACTIVATOR IN COMPLEX WITH EGR-CMK (GLU-GLY-ARG CHLOROMETHYL KETONE)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Catalytic domain structure of vampire bat plasminogen activator: a molecular paradigm for proteolysis without activation cleavage.

Renatus, M.Stubbs, M.T.Huber, R.Bringmann, P.Donner, P.Schleuning, W.D.Bode, W.

(1997) Biochemistry 36: 13483-13493

  • DOI: 10.1021/bi971129x
  • Primary Citation of Related Structures:  
    1A5I

  • PubMed Abstract: 
  • The saliva of the blood-eating vampire bat Desmodus rotundus contains plasminogen activators (PAs) that maintain the fluidity of the prey's blood by activating plasminogen and dissolving developing fibrin clots. D. rotundus salivary PAs (DSPAs) are c ...

    The saliva of the blood-eating vampire bat Desmodus rotundus contains plasminogen activators (PAs) that maintain the fluidity of the prey's blood by activating plasminogen and dissolving developing fibrin clots. D. rotundus salivary PAs (DSPAs) are composed of evolutionarily conserved domains reminiscent of human tissue-type PA (tPA), but their catalytic domain lacks a plasmin-sensitive "activation cleavage site". Despite this, all DSPAs are intrinsically active and enormously stimulated in the presence of fibrin. The recombinant catalytic domain of DSPAalpha1 has been crystallized in a covalent complex with Glu-Gly-Arg-chloromethyl ketone and its structure solved at 2.9 A resolution. The structure is similar to that of activated two-chain human tPA. Despite its single-chain status, the activation domain is observed in an enzymatically active conformation, with a functional substrate binding site and active site accommodating the peptidylmethylene inhibitor. The activation pocket, which normally receives the N-terminal Ile16, is occupied by the side chain of Lys156, whose distal ammonium group makes an internal salt bridge with the carboxylate group of Asp194. Lys156 is in a groove shielded from the bulk solvent by the intact "activation loop" (Gln10-Phe21), favoring Lys156-Asp194 salt bridge formation and stabilization of a functional substrate binding site. Together with the characteristic 186 insertion loop, the activation loop could act as a switch, effecting full single-chain enzymatic activity upon binding to fibrin.


    Related Citations: 
    • Lysine 156 Promotes the Anomalous Proenzyme Activity of Tpa: X-Ray Crystal Structure of Single-Chain Human Tpa
      Renatus, M., Engh, R.A., Stubbs, M.T., Huber, R., Fischer, S., Kohnert, U., Bode, W.
      (1997) EMBO J 16: 4797
    • Tissue-Type Plasminogen Activator: Variants and Crystal/Solution Structures Demarcate Structural Determinants of Function
      Bode, W., Renatus, M.
      (1997) Curr Opin Struct Biol 7: 865
    • The 2.3 A Crystal Structure of the Catalytic Domain of Recombinant Two-Chain Human Tissue-Type Plasminogen Activator
      Lamba, D., Bauer, M., Huber, R., Fischer, S., Rudolph, R., Kohnert, U., Bode, W.
      (1996) J Mol Biol 258: 117

    Organizational Affiliation

    Department of Structural Research, Max-Planck-Institute of Biochemistry, Martinsried, Germany. renatus@biochem.mpg.de



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PLASMINOGEN ACTIVATORA265Desmodus rotundusMutation(s): 0 
EC: 3.4.21.68
Find proteins for P98119 (Desmodus rotundus)
Explore P98119 
Go to UniProtKB:  P98119
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0GJ
Query on 0GJ

Download CCD File 
A
L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide
C14 H28 Cl N6 O5
XELWNHKFCNMWQO-LPEHRKFASA-O
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000288 (0GJ)
Query on PRD_000288
AGLU-GLY-ARG-CHLOROMETHYL KETONEPeptide-like /  Inhibitor

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.86α = 90
b = 73.86β = 90
c = 135.19γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
ROTAVATAdata reduction
X-PLORmodel building
X-PLORrefinement
CCP4data scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-03-23
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other