4A1O | pdb_00004a1o

Crystal structure of Mycobacterium tuberculosis PurH complexed with AICAR and a novel nucleotide CFAIR, at 2.48 A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 
    0.227 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.182 (Depositor) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structural Analyses of a Purine Biosynthetic Enzyme from Mycobacterium Tuberculosis Reveal a Novel Bound Nucleotide.

Le Nours, J.Bulloch, E.M.M.Zhang, Z.Greenwood, D.R.Middleditch, M.J.Dickson, J.M.J.Baker, E.N.

(2011) J Biological Chem 286: 40706

  • DOI: https://doi.org/10.1074/jbc.M111.291138
  • Primary Citation Related Structures: 
    3ZZM, 4A1O

  • PubMed Abstract: 

    Enzymes of the de novo purine biosynthetic pathway have been identified as essential for the growth and survival of Mycobacterium tuberculosis and thus have potential for the development of anti-tuberculosis drugs. The final two steps of this pathway are carried out by the bifunctional enzyme 5-aminoimidazole-4-carboxamide ribonucleotide transformylase/inosine monophosphate cyclohydrolase (ATIC), also known as PurH. This enzyme has already been the target of anti-cancer drug development. We have determined the crystal structures of the M. tuberculosis ATIC (Rv0957) both with and without the substrate 5-aminoimidazole-4-carboxamide ribonucleotide, at resolutions of 2.5 and 2.2 Å, respectively. As for other ATIC enzymes, the protein is folded into two domains, the N-terminal domain (residues 1-212) containing the cyclohydrolase active site and the C-terminal domain (residues 222-523) containing the formyltransferase active site. An adventitiously bound nucleotide was found in the cyclohydrolase active site in both structures and was identified by NMR and mass spectral analysis as a novel 5-formyl derivative of an earlier intermediate in the biosynthetic pathway 4-carboxy-5-aminoimidazole ribonucleotide. This result and other studies suggest that this novel nucleotide is a cyclohydrolase inhibitor. The dimer formed by M. tuberculosis ATIC is different from those seen for human and avian ATICs, but it has a similar ∼50-Å separation of the two active sites of the bifunctional enzyme. Evidence in M. tuberculosis ATIC for reactivity of half-the-sites in the cyclohydrolase domains can be attributed to ligand-induced movements that propagate across the dimer interface and may be a common feature of ATIC enzymes.


  • Organizational Affiliation
    • Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.

Macromolecule Content 

  • Total Structure Weight: 111.58 kDa 
  • Atom Count: 8,032 
  • Modeled Residue Count: 1,033 
  • Deposited Residue Count: 1,046 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BIFUNCTIONAL PURINE BIOSYNTHESIS PROTEIN PURH
A, B
523Mycobacterium tuberculosis H37RvMutation(s): 0 
EC: 2.1.2.3 (PDB Primary Data), 3.5.4.10 (PDB Primary Data)
UniProt
Find proteins for P9WHM7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHM7 
Go to UniProtKB:  P9WHM7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WHM7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JLN

Query on JLN



Download:Ideal Coordinates CCD File
G [auth A]5-(FORMYLAMINO)-1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-1H-IMIDAZOLE-4-CARBOXYLIC ACID
C10 H14 N3 O10 P
UEBVPQPUWAADHX-FJGDRVTGSA-N
AMZ

Query on AMZ



Download:Ideal Coordinates CCD File
D [auth A],
I [auth B]
AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE
C9 H15 N4 O8 P
NOTGFIUVDGNKRI-UUOKFMHZSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
J [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
K

Query on K



Download:Ideal Coordinates CCD File
C [auth A],
H [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free:  0.227 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.182 (Depositor) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.258α = 90
b = 107.883β = 90
c = 130.924γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-28
    Type: Initial release
  • Version 1.1: 2011-10-26
    Changes: Database references
  • Version 1.2: 2011-12-14
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description