5M8H

ATP phosphoribosyltransferase (HisZG ATPPRT) from Psychrobacter arcticus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.230 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Kinetics and Structure of a Cold-Adapted Hetero-Octameric ATP Phosphoribosyltransferase.

Stroek, R.Ge, Y.Talbot, P.D.Glok, M.K.Bernas, K.E.Thomson, C.M.Gould, E.R.Alphey, M.S.Liu, H.Florence, G.J.Naismith, J.H.da Silva, R.G.

(2017) Biochemistry 56: 793-803

  • DOI: https://doi.org/10.1021/acs.biochem.6b01138
  • Primary Citation of Related Structures:  
    5M8H

  • PubMed Abstract: 

    Adenosine 5'-triphosphate phosphoribosyltransferase (ATPPRT) catalyzes the first step in histidine biosynthesis, the condensation of ATP and 5-phospho-α-d-ribosyl-1-pyrophosphate to generate N 1 -(5-phospho-β-d-ribosyl)-ATP and inorganic pyrophosphate. The enzyme is allosterically inhibited by histidine. Two forms of ATPPRT, encoded by the hisG gene, exist in nature, depending on the species. The long form, HisG L , is a single polypeptide chain with catalytic and regulatory domains. The short form, HisG S , lacks a regulatory domain and cannot bind histidine. HisG S instead is found in complex with a regulatory protein, HisZ, constituting the ATPPRT holoenzyme. HisZ triggers HisG S catalytic activity while rendering it sensitive to allosteric inhibition by histidine. Until recently, HisG S was thought to be catalytically inactive without HisZ. Here, recombinant HisG S and HisZ from the psychrophilic bacterium Psychrobacter arcticus were independently overexpressed and purified. The crystal structure of P. arcticus ATPPRT was determined at 2.34 Å resolution, revealing an equimolar HisG S -HisZ hetero-octamer. Steady-state kinetics indicate that both the ATPPRT holoenzyme and HisG S are catalytically active. Surprisingly, HisZ confers only a modest 2-4-fold increase in k cat . Reaction profiles for both enzymes cannot be distinguished by 31 P nuclear magnetic resonance, indicating that the same reaction is catalyzed. The temperature dependence of k cat shows deviation from Arrhenius behavior at 308 K with the holoenzyme. Interestingly, such deviation is detected only at 313 K with HisG S . Thermal denaturation by CD spectroscopy resulted in T m 's of 312 and 316 K for HisZ and HisG S , respectively, suggesting that HisZ renders the ATPPRT complex more thermolabile. This is the first characterization of a psychrophilic ATPPRT.


  • Organizational Affiliation

    School of Engineering and Applied Science, Rotterdam University of Applied Science , G. J. de Jonghweg 4-6, 3015 GG Rotterdam, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP phosphoribosyltransferase regulatory subunit
A, B, C, D
388Psychrobacter arcticus 273-4Mutation(s): 0 
Gene Names: hisZPsyc_0676
UniProt
Find proteins for Q4FTX3 (Psychrobacter arcticus (strain DSM 17307 / VKM B-2377 / 273-4))
Explore Q4FTX3 
Go to UniProtKB:  Q4FTX3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4FTX3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP phosphoribosyltransferase
E, F, G, H
232Psychrobacter arcticus 273-4Mutation(s): 0 
Gene Names: hisGPsyc_1903
EC: 2.4.2.17
UniProt
Find proteins for Q4FQF7 (Psychrobacter arcticus (strain DSM 17307 / VKM B-2377 / 273-4))
Explore Q4FQF7 
Go to UniProtKB:  Q4FQF7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4FQF7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
BA [auth C]
CA [auth C]
HA [auth D]
IA [auth D]
M [auth A]
BA [auth C],
CA [auth C],
HA [auth D],
IA [auth D],
M [auth A],
MA [auth E],
N [auth A],
O [auth A],
QA [auth G],
U [auth B],
V [auth B],
W [auth B]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
SR
Query on SR

Download Ideal Coordinates CCD File 
DA [auth D]
EA [auth D]
FA [auth D]
I [auth A]
J [auth A]
DA [auth D],
EA [auth D],
FA [auth D],
I [auth A],
J [auth A],
P [auth B],
Q [auth B],
X [auth C],
Y [auth C],
Z [auth C]
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth C]
GA [auth D]
JA [auth E]
K [auth A]
KA [auth E]
AA [auth C],
GA [auth D],
JA [auth E],
K [auth A],
KA [auth E],
L [auth A],
LA [auth E],
NA [auth F],
OA [auth F],
PA [auth G],
R [auth B],
RA [auth H],
S [auth B],
SA [auth H],
T [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.02α = 90
b = 146.73β = 102.4
c = 101.9γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
University of St. AndrewsUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Source and taxonomy
  • Version 1.2: 2024-01-17
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description