Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.02 kDa 
• Atom Count: 3205 
• Modelled Residue Count: 386 
• Deposited Residue Count: 388 
• Unique protein chains: 1

1FC6

PHOTOSYSTEM II D1 C-TERMINAL PROCESSING PROTEASE

• PDB DOI: 10.2210/pdb1FC6/pdb

• Classification: HYDROLASE
• Organism(s): Tetradesmus obliquus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2000-07-18 Released: 2001-01-18 
• Deposition Author(s): Liao, D.I., Qian, J., Chisholm, D.A., Jordan, D.B., Diner, B.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.237 
• R-Value Work: 0.168 

Literature

Crystal structures of the photosystem II D1 C-terminal processing protease.

Liao, D.I., Qian, J., Chisholm, D.A., Jordan, D.B., Diner, B.A.

(2000) Nat Struct Biol 7: 749-753

• PubMed: 10966643 
• DOI: 10.1038/78973
• Primary Citation of Related Structures:  
  1FC6, 1FC7, 1FC9, 1FCF


• PubMed Abstract: 
  

We report here the first three-dimensional structure of the D1 C-terminal processing protease (D1P), which is encoded by the ctpA gene. This enzyme removes the C-terminal extension of the D1 polypeptide of photosystem II of oxygenic photosynthesis. Proteolytic processing is necessary to allow the light driven assembly of the tetranuclear manganese cluster, which is responsible for photosynthetic water oxidation. The X-ray structure of the Scenedesmus obliquus enzyme has been determined at 1.8 A resolution using the multiwavelength anomalous dispersion method. The enzyme is monomeric and is composed of three folding domains. The middle domain is topologically homologous to known PDZ motifs and is proposed to be the site at which the substrate C-terminus binds. The remainder of the substrate likely extends across the face of the enzyme, interacting at its scissile bond with the enzyme active site Ser 372 / Lys 397 catalytic dyad, which lies at the center of the protein at the interface of the three domains.

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Organizational Affiliation: 

E. I. du Pont de Nemours & Company, Central Research and Development, Experimental Station, Wilmington, Delaware 19880, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOTOSYSTEM II D1 PROTEASE	A	388	Tetradesmus obliquus	Mutation(s): 4  Gene Names: ctpA, D1P EC: 3.4.21.102
UniProt
Find proteins for O04073 (Tetradesmus obliquus) Explore O04073  Go to UniProtKB:  O04073

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.237 
• R-Value Work: 0.168 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.3	α = 90
b = 64.45	β = 122.11
c = 63.73	γ = 90

Software Package:

Software Name	Purpose
PHASES	phasing
TNT	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-07-18 
• Released Date: 2001-01-18 
Deposition Author(s): Liao, D.I., Qian, J., Chisholm, D.A., Jordan, D.B., Diner, B.A.

Revision History  

• Version 1.0: 2001-01-18
  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: 2021-11-03
  Changes: Database references, Derived calculations