4YB6

Adenosine triphosphate phosphoribosyltransferase from Campylobacter jejuni in complex with the inhibitors AMP and histidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Campylobacter jejuni adenosine triphosphate phosphoribosyltransferase is an active hexamer that is allosterically controlled by the twisting of a regulatory tail.

Mittelstadt, G.Moggre, G.J.Panjikar, S.Nazmi, A.R.Parker, E.J.

(2016) Protein Sci 25: 1492-1506

  • DOI: https://doi.org/10.1002/pro.2948
  • Primary Citation of Related Structures:  
    4YB5, 4YB6, 4YB7

  • PubMed Abstract: 

    Adenosine triphosphate phosphoribosyltransferase (ATP-PRT) catalyzes the first committed step of the histidine biosynthesis in plants and microorganisms. Here, we present the functional and structural characterization of the ATP-PRT from the pathogenic ε-proteobacteria Campylobacter jejuni (CjeATP-PRT). This enzyme is a member of the long form (HisGL ) ATP-PRT and is allosterically inhibited by histidine, which binds to a remote regulatory domain, and competitively inhibited by AMP. In the crystalline form, CjeATP-PRT was found to adopt two distinctly different hexameric conformations, with an open homohexameric structure observed in the presence of substrate ATP, and a more compact closed form present when inhibitor histidine is bound. CjeATP-PRT was observed to adopt only a hexameric quaternary structure in solution, contradicting previous hypotheses favoring an allosteric mechanism driven by an oligomer equilibrium. Instead, this study supports the conclusion that the ATP-PRT long form hexamer is the active species; the tightening of this structure in response to remote histidine binding results in an inhibited enzyme.


  • Organizational Affiliation

    Maurice Wilkins Centre, Biomolecular Interaction Centre, Christchurch, 8140, New Zealand.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP phosphoribosyltransferase
A, B, C, D, E
A, B, C, D, E, F
300Campylobacter jejuni RM1221Mutation(s): 0 
Gene Names: hisGCJE1769
EC: 2.4.2.17
UniProt
Find proteins for Q5HSJ4 (Campylobacter jejuni (strain RM1221))
Explore Q5HSJ4 
Go to UniProtKB:  Q5HSJ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5HSJ4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download Ideal Coordinates CCD File 
DA [auth F]
G [auth A]
K [auth B]
O [auth C]
T [auth D]
DA [auth F],
G [auth A],
K [auth B],
O [auth C],
T [auth D],
X [auth E]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
HIS
Query on HIS

Download Ideal Coordinates CCD File 
EA [auth F]
H [auth A]
L [auth B]
P [auth C]
U [auth D]
EA [auth F],
H [auth A],
L [auth B],
P [auth C],
U [auth D],
Y [auth E]
HISTIDINE
C6 H10 N3 O2
HNDVDQJCIGZPNO-YFKPBYRVSA-O
PEG
Query on PEG

Download Ideal Coordinates CCD File 
FA [auth F]
I [auth A]
M [auth B]
Q [auth C]
V [auth D]
FA [auth F],
I [auth A],
M [auth B],
Q [auth C],
V [auth D],
Z [auth E]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
CA [auth E]
GA [auth F]
J [auth A]
AA [auth E],
BA [auth E],
CA [auth E],
GA [auth F],
J [auth A],
N [auth B],
R [auth C],
S [auth C],
W [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.871α = 90
b = 124.906β = 115.86
c = 92.809γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata 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: 2016-03-09
    Type: Initial release
  • Version 1.1: 2017-11-01
    Changes: Author supporting evidence, Data collection, Derived calculations
  • Version 1.2: 2018-09-05
    Changes: Data collection, Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description