1BDA

CATALYTIC DOMAIN OF HUMAN SINGLE CHAIN TISSUE PLASMINOGEN ACTIVATOR IN COMPLEX WITH DANSYL-EGR-CMK (DANSYL-GLU-GLY-ARG CHLOROMETHYL KETONE)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

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: 4797-4805

  • DOI: 10.1093/emboj/16.16.4797
  • Primary Citation of Related Structures:  
    1BDA

  • PubMed Abstract: 

    • Tissue type plasminogen activator (tPA) is the physiological initiator of fibrinolysis, activating plasminogen via highly specific proteolysis; plasmin then degrades fibrin with relatively broad specificity. Unlike other chymotrypsin family serine protei ...

    Tissue type plasminogen activator (tPA) is the physiological initiator of fibrinolysis, activating plasminogen via highly specific proteolysis; plasmin then degrades fibrin with relatively broad specificity. Unlike other chymotrypsin family serine proteinases, tPA is proteolytically active in a single-chain form. This form is also preferred for therapeutic administration of tPA in cases of acute myocardial infarction. The proteolytic cleavage which activates most other chymotrypsin family serine proteinases increases the catalytic efficiency of tPA only 5- to 10-fold. The X-ray crystal structure of the catalytic domain of recombinant human single-chain tPA shows that Lys156 forms a salt bridge with Asp194, promoting an active conformation in the single-chain form. Comparisons with the structures of other serine proteinases that also possess Lys156, such as trypsin, factor Xa and human urokinase plasminogen activator (uPA), identify a set of secondary interactions which are required for Lys156 to fulfil this activating role. These findings help explain the anomalous single-chain activity of tPA and may suggest strategies for design of new therapeutic plasminogen activators.

    Related Citations: 
    • 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
    • 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: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SINGLE CHAIN TISSUE TYPE PLASMINOGEN ACTIVATOR A, B265Homo sapiensMutation(s): 0 
Gene Names: PLAT
EC: 3.4.21.68
Find proteins for P00750 (Homo sapiens)
Explore P00750 
Go to UniProtKB:  P00750
NIH Common Fund Data Resources
PHAROS:  P00750
GTEx:  ENSG00000104368
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2Z0
Query on 2Z0
Download Ideal Coordinates CCD File 
A, B
N-{[5-(dimethylamino)naphthalen-2-yl]sulfonyl}-L-alpha-glutamyl-N-[(1S)-4-{[amino(iminio)methyl]amino}-1-(chloroacetyl) butyl]glycinamide
C26 H37 Cl N7 O7 S
VKQAIOBCWDJDIP-PMACEKPBSA-O		 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000413 (2Z0)
Query on PRD_000413		A, Bdansylglutamyl-glycyl-arginine chloromethyl ketonePeptide-like /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.99α = 90
b = 80.78β = 90
c = 159.16γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
ROTAGRdata reduction
X-PLORmodel building
X-PLORrefinement
ROTAGRdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-05-11
    Type: Initial release
  • Version 1.1: 2008-05-22
    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