3U55

Crystal structure (Type-2) of SAICAR synthetase from Pyrococcus horikoshii OT3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

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This is version 1.1 of the entry. See complete history


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

  • DOI: 10.1016/j.ijbiomac.2012.10.028
  • Primary Citation of 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 ...

    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.


    Organizational Affiliation

    Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphoribosylaminoimidazole-succinocarboxamide synthaseA238Pyrococcus horikoshii OT3Mutation(s): 0 
Gene Names: PH0239purC
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO57978
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
D [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.1α = 90
b = 155.39β = 90
c = 78.35γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2013-12-18
    Changes: Database references