1KUT

Structural Genomics, Protein TM1243, (SAICAR synthetase)

• PDB DOI: https://doi.org/10.2210/pdb1KUT/pdb

• Classification: STRUCTURAL GENOMICS, LIGASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2002-01-22 Released: 2002-08-14 
• Deposition Author(s): Zhang, R., Skarina, T., Beasley, S., Edwards, A., Joachimiak, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.281 (Depositor), 0.358 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.363 (DCC) 

Literature

Structure of SAICAR synthase from Thermotoga maritima at 2.2 angstroms reveals an unusual covalent dimer.

Zhang, R., Skarina, T., Evdokimova, E., Edwards, A., Savchenko, A., Laskowski, R., Cuff, M.E., Joachimiak, A.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 335-339

• PubMed: 16582479 
• DOI: https://doi.org/10.1107/S1744309106009651
• Primary Citation of Related Structures:  
  1KUT


• PubMed Abstract: 
  

  As a part of a structural genomics program, the 2.2 angstroms resolution crystal structure of the PurC gene product from Thermotoga maritima has been solved. This 26.2 kDa protein belongs to the phophoribosylaminoimidazole-succinocarboxamide or SAICAR synthase family of enzymes, the members of which are involved in de novo purine biosynthesis. SAICAR synthase can be divided into three subdomains: two alpha+beta regions exhibiting structural homology with ATP-binding proteins and a carboxy-terminal subdomain of two alpha-helices. The asymmetric unit contains two copies of the protein which are covalently linked by a disulfide bond between Cys126(A) and Cys126(B). This 230-amino-acid protein exhibits high structural homology with SAICAR synthase from baker's yeast. The protein structure is described and compared with that of the ATP-SAICAR synthase complex from yeast.

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Organizational Affiliation: 

Biosciences Division, Midwest Center for Structural Genomics, Structural Biology Center, Argonne National Laboratory, Argonne, IL 60439, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 53.02 kDa 
• Atom Count: 3,583 
• Modelled Residue Count: 435 
• Deposited Residue Count: 460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylaminoimidazole-succinocarboxamide synthase	A, B	230	Thermotoga maritima	Mutation(s): 5  Gene Names: TM1243 EC: 6.3.2.6
UniProt
Find proteins for Q9X0X0 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X0X0  Go to UniProtKB:  Q9X0X0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.281 (Depositor), 0.358 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.363 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.509	α = 90
b = 43.067	β = 92.3
c = 80.217	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
HKL-2000	data reduction
CNS	refinement
d*TREK	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-08-14 
Deposition Author(s): Zhang, R., Skarina, T., Beasley, S., Edwards, A., Joachimiak, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2002-08-14
  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: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary