3U54 | pdb_00003u54

Crystal structure (Type-1) of SAICAR synthetase from Pyrococcus horikoshii OT3

• PDB DOI: https://doi.org/10.2210/pdb3U54/pdb

• Classification: LIGASE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-10-11 Released: 2012-10-17 
• Deposition Author(s): Manjunath, K., Kanaujia, S.P., Kanagaraj, S., Jeyakanthan, J., Sekar, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.286 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

Structure of SAICAR synthetase from Pyrococcus horikoshii OT3: insights into thermal stability

Manjunath, K., Kanaujia, S.P., Kanagaraj, S., Jeyakanthan, J., Sekar, K.

(2013) Int J Biol Macromol 53: 7-19

• PubMed: 23137517 
• DOI: https://doi.org/10.1016/j.ijbiomac.2012.10.028
• Primary Citation Related Structures: 
  3U54, 3U55


• PubMed Abstract: 
  

  The first native crystal structure of Phosphoribosylaminoimidazole-succinocarboxamide synthetase (SAICAR synthetase) from a hyperthermophilic organism Pyrococcus horikoshii OT3 was determined in two space groups H3 (Type-1: Resolution 2.35Å) and in C222(1) (Type-2: Resolution 1.9Å). Both are dimeric but Type-1 structure exhibited hexameric arrangement due to the presence of cadmium ions. A comparison has been made on the sequence and structures of all SAICAR synthetases to better understand the differences between mesophilic, thermophilic and hyperthermophilic SAICAR synthetases. These SAICAR synthetases are reasonably similar in sequence and three-dimensional structure; however, differences were visible only in the subtler details of percentage composition of the sequences, salt bridge interactions and non-polar contact areas.

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Organizational Affiliation: 
• Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 57.31 kDa 
• Atom Count: 3,740 
• Modeled Residue Count: 450 
• Deposited Residue Count: 476 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylaminoimidazole-succinocarboxamide synthase	A, B	238	Pyrococcus horikoshii OT3	Mutation(s): 0  Gene Names: PH0239, purC EC: 6.3.2.6
UniProt
Find proteins for O57978 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57978  Go to UniProtKB:  O57978

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4	D [auth A], K [auth A], R [auth B], S [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BU1	C [auth A]	1,4-BUTANEDIOL C4 H10 O2 WERYXYBDKMZEQL-UHFFFAOYSA-N
ACT	T [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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: 2.35 Å
• R-Value Free:  0.286 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.42	α = 90
b = 95.42	β = 90
c = 148.631	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-17 
Deposition Author(s): Manjunath, K., Kanaujia, S.P., Kanagaraj, S., Jeyakanthan, J., Sekar, K.

Revision History  

• Version 1.0: 2012-10-17
  Type: Initial release
  
• Version 1.1: 2013-12-18
  Changes: Database references
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-11-13
  Changes: Structure summary