1KA4 | pdb_00001ka4

Structure of Pyrococcus furiosus carboxypeptidase Nat-Pb

• PDB DOI: https://doi.org/10.2210/pdb1KA4/pdb

• Classification: carboxypeptidase
• Organism(s): Pyrococcus furiosus
• Mutation(s): No 


• Deposited: 2001-10-31 Released: 2002-11-06 
• Deposition Author(s): Arndt, J.W., Hao, B., Ramakrishnan, V., Cheng, T., Chan, S.I., Chan, M.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.276 (Depositor) 
• R-Value Work: 
  0.236 (Depositor) 
• R-Value Observed: 
  0.236 (Depositor) 

Literature

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

• PubMed: 11839307 
• DOI: https://doi.org/10.1016/s0969-2126(02)00698-6
• Primary Citation 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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 59.33 kDa 
• Atom Count: 4,247 
• Modeled Residue Count: 497 
• Deposited Residue Count: 499 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
M32 carboxypeptidase	A	499	Pyrococcus furiosus	Mutation(s): 0  EC: 3.4.17.19
UniProt
Find proteins for Q8U3L0 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U3L0  Go to UniProtKB:  Q8U3L0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PB	B [auth A]	LEAD (II) ION Pb RVPVRDXYQKGNMQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.276 (Depositor) 
• R-Value Work:  0.236 (Depositor) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.3	α = 90
b = 67.582	β = 95.2
c = 67.185	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-11-06 
Deposition Author(s): Arndt, J.W., Hao, B., Ramakrishnan, V., Cheng, T., Chan, S.I., Chan, M.K.

Revision History  

• 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: 2024-02-07
  Changes: Data collection, Database references, Derived calculations