4FE2

X-Ray Structure of SAICAR Synthetase (PurC) from Streptococcus pneumoniae complexed with AIR, ADP, Asp and Mg2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.201 

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This is version 1.2 of the entry. See complete history


Literature

Structures of SAICAR synthetase (PurC) from Streptococcus pneumoniae with ADP, Mg(2+), AIR and Asp.

Wolf, N.M.Abad-Zapatero, C.Johnson, M.E.Fung, L.W.

(2014) Acta Crystallogr D Biol Crystallogr 70: 841-850

  • DOI: https://doi.org/10.1107/S139900471303366X
  • Primary Citation of Related Structures:  
    4FE2, 4NYE

  • PubMed Abstract: 

    Streptococcus pneumoniae is a multidrug-resistant pathogen that is a target of considerable interest for antibacterial drug development. One strategy for drug discovery is to inhibit an essential metabolic enzyme. The seventh step of the de novo purine-biosynthesis pathway converts carboxyaminoimidazoleribonucleotide (CAIR) and L-aspartic acid (Asp) to 4-(N-succino)-5-aminoimidazole-4-carboxamide ribonucleotide (SAICAR) in the presence of adenosine 5'-triphosphate (ATP) using the enzyme PurC. PurC has been shown to be conditionally essential for bacterial replication. Two crystal structures of this essential enzyme from Streptococcus pneumoniae (spPurC) in the presence of adenosine 5'-diphosphate (ADP), Mg(2+), aminoimidazoleribonucleotide (AIR) and/or Asp have been obtained. This is the first structural study of spPurC, as well as the first of PurC from any species with Asp in the active site. Based on these findings, two model structures are proposed for the active site with all of the essential ligands (ATP, Mg(2+), Asp and CAIR) present, and a relay mechanism for the formation of the product SAICAR is suggested.


  • Organizational Affiliation

    Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoribosylaminoimidazole-succinocarboxamide synthase
A, B
255Streptococcus pneumoniaeMutation(s): 0 
Gene Names: purCSP_0044
EC: 6.3.2.6
UniProt
Find proteins for Q07296 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore Q07296 
Go to UniProtKB:  Q07296
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07296
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
D [auth A],
L [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
AIR
Query on AIR

Download Ideal Coordinates CCD File 
C [auth A],
K [auth B]
5-AMINOIMIDAZOLE RIBONUCLEOTIDE
C8 H14 N3 O7 P
PDACUKOKVHBVHJ-XVFCMESISA-N
ASP
Query on ASP

Download Ideal Coordinates CCD File 
H [auth A]ASPARTIC ACID
C4 H7 N O4
CKLJMWTZIZZHCS-REOHCLBHSA-N
144
Query on 144

Download Ideal Coordinates CCD File 
F [auth A],
I [auth A],
J [auth A],
N [auth B]
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM
C4 H12 N O3
DRDCQJADRSJFFD-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
O [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

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G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
M [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.074α = 90
b = 65.021β = 92.09
c = 86.052γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2014-04-02
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description