3OD5

Crystal structure of active caspase-6 bound with Ac-VEID-CHO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of human caspase 6 reveal a new mechanism for intramolecular cleavage self-activation

Wang, X.-J.Cao, Q.Liu, X.Wang, K.-T.Mi, W.Zhang, Y.Li, L.-F.Leblanc, A.C.Su, X.-D.

(2010) EMBO Rep 11: 841-847

  • DOI: 10.1038/embor.2010.141
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Dimeric effectors caspase 3 and caspase 7 are activated by initiator caspase processing. In this study, we report the crystal structures of effector caspase 6 (CASP6) zymogen and N-Acetyl-Val-Glu-Ile-Asp-al-inhibited CASP6. Both of these forms of CAS ...

    Dimeric effectors caspase 3 and caspase 7 are activated by initiator caspase processing. In this study, we report the crystal structures of effector caspase 6 (CASP6) zymogen and N-Acetyl-Val-Glu-Ile-Asp-al-inhibited CASP6. Both of these forms of CASP6 have a dimeric structure, and in CASP6 zymogen the intersubunit cleavage site (190)TEVD(193) is well structured and inserts into the active site. This positions residue Asp 193 to be easily attacked by the catalytic residue Cys 163. We demonstrate biochemically that intramolecular cleavage at Asp 193 is a prerequisite for CASP6 self-activation and that this activation mechanism is dependent on the length of the L2 loop. Our results indicate that CASP6 can be activated and regulated through intramolecular self-cleavage.


    Organizational Affiliation

    National Laboratory of Protein Engineering & Plant Genetic Engineering, Peking University, Haidian District, Beijing, People's Republic of China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Caspase-6A, B278Homo sapiensMutation(s): 0 
Gene Names: CASP6MCH2
EC: 3.4.22.59
Find proteins for P55212 (Homo sapiens)
Explore P55212 
Go to UniProtKB:  P55212
NIH Common Fund Data Resources
PHAROS  P55212
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
peptide aldehyde inhibitor AC-VEID-CHOC, D5N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAC
Query on CAC

Download CCD File 
A, B
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000976
Query on PRD_000976
C, DN-acetyl-L-valyl-L-alpha-glutamyl-N-[(2S)-1-carboxy-3-oxopropan-2-yl]-L-isoleucinamideP /  Inhibitor

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Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ASA
Query on ASA
C,DL-PEPTIDE LINKINGC4 H7 N O3ASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.464α = 90
b = 89.589β = 111.67
c = 61.145γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-12-12
    Changes: Other