Structure of Pyrococcus furiosus Carboxypeptidase Apo-Mg

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 

Starting Model: experimental
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Crystal Structure of a Novel Carboxypeptidase from the Hyperthermophilic Archaeon Pyrococcus furiosus

Arndt, J.W.Hao, B.Ramakrishnan, V.Cheng, T.Chan, S.I.Chan, M.K.

(2002) Structure 10: 215-224

  • DOI: https://doi.org/10.1016/s0969-2126(02)00698-6
  • Primary Citation of Related Structures:  
    1K9X, 1KA2, 1KA4

  • PubMed Abstract: 

    The structure of Pyrococcus furiosus carboxypeptidase (PfuCP) has been determined to 2.2 A resolution using multiwavelength anomalous diffraction (MAD) methods. PfuCP represents the first structure of the new M32 family of carboxypeptidases. The overall structure is comprised of a homodimer. Each subunit is mostly helical with its most pronounced feature being a deep substrate binding groove. The active site lies at the bottom of this groove and contains an HEXXH motif that coordinates the metal ion required for catalysis. Surprisingly, the structure is similar to the recently reported rat neurolysin. Comparison of these structures as well as sequence analyses with other homologous proteins reveal several conserved residues. The roles for these conserved residues in the catalytic mechanism are inferred based on modeling and their location.

  • Organizational Affiliation

    Department of Chemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
M32 carboxypeptidase499Pyrococcus furiosusMutation(s): 0 
Find proteins for Q8U3L0 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U3L0 
Go to UniProtKB:  Q8U3L0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U3L0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MG

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.515α = 90
b = 67.106β = 95.88
c = 67.885γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description