2F9P

Crystal Structure of the Recombinant Human Alpha I Tryptase Mutant D216G in Complex with Leupeptin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

X-ray Structures of Free and Leupeptin-complexed Human alpha I-Tryptase Mutants: Indication for an alpha to beta-Tryptase Transition

Rohr, K.B.Selwood, T.Marquardt, U.Huber, R.Schechter, N.M.Bode, W.Than, M.E.

(2005) J.Mol.Biol. 357: 195-209

  • DOI: 10.1016/j.jmb.2005.12.037
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tryptases alpha and beta are trypsin-like serine proteinases expressed in large amounts by mast cells. Beta-tryptase is a tetramer that has enzymatic activity, but requires heparin binding to maintain functional and structural stability, whereas alph ...

    Tryptases alpha and beta are trypsin-like serine proteinases expressed in large amounts by mast cells. Beta-tryptase is a tetramer that has enzymatic activity, but requires heparin binding to maintain functional and structural stability, whereas alpha-tryptase has little, if any, enzymatic activity but is a stable tetramer in the absence of heparin. As shown previously, these differences can be mainly attributed to the different conformations of the 214-220 segment. Interestingly, the replacement of Asp216 by Gly, which is present in beta-tryptase, results in enzymatically active but less stable alpha-tryptase mutants. We have solved the crystal structures of both the single (D216G) and the double (K192Q/D216G) mutant forms of recombinant human alphaI-tryptase in complex with the peptide inhibitor leupeptin, as well as the structure of the non-inhibited single mutant. The inhibited mutants exhibited an open functional substrate binding site, while in the absence of an inhibitor, the open (beta-tryptase-like) and the closed (alpha-tryptase-like) conformations were present simultaneously. This shows that both forms are in a two-state equilibrium, which is influenced by the residues in the vicinity of the active site and by inhibitor/substrate binding. Novel insights regarding the observed stability differences as well as a potential proteolytic activity of wild-type alpha-tryptase, which may possess a cryptic active site, are discussed.


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18, 82152 Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tryptase alpha-1
A, B, C, D
245Homo sapiensMutation(s): 2 
Gene Names: TPSAB1 (TPS1, TPS2, TPSB1)
EC: 3.4.21.59
Find proteins for Q15661 (Homo sapiens)
Go to Gene View: TPSAB1
Go to UniProtKB:  Q15661
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Leupeptin
E, F, G, H
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BU3
Query on BU3

Download SDF File 
Download CCD File 
A, B, C, D
(R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
D
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
B, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000216 (SVC)
Query on PRD_000216
E,F,G,HLEUPEPTINOligopeptide / Enzyme inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 83.300α = 90.00
b = 88.230β = 90.00
c = 162.870γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-31
    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