1USY | pdb_00001usy

ATP phosphoribosyl transferase (HisG:HisZ) complex from Thermotoga maritima


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 
    0.287 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Regulation of the Hetero-Octameric ATP Phosphoribosyl Transferase Complex from Thermotoga Maritima by a tRNA Synthetase-Like Subunit.

Vega, M.C.Zou, P.Fernandez, F.J.Murphy, G.E.Sterner, R.Popov, A.Wilmanns, M.

(2005) Mol Microbiol 55: 675

  • DOI: https://doi.org/10.1111/j.1365-2958.2004.04422.x
  • Primary Citation Related Structures: 
    1USY

  • PubMed Abstract: 

    The molecular structure of the ATP phosphoribosyl transferase from the hyperthermophile Thermotoga maritima is composed of a 220 kDa hetero-octameric complex comprising four catalytic subunits (HisGS) and four regulatory subunits (HisZ). Steady-state kinetics indicate that only the complete octameric complex is active and non-competitively inhibited by the pathway product histidine. The rationale for these findings is provided by the crystal structure revealing a total of eight histidine binding sites that are located within each of the four HisGS-HisZ subunit interfaces formed by the ATP phosphoribosyl transferase complex. While the structure of the catalytic HisGS subunit is related to the catalytic domain of another family of (HisGL)2 ATP phosphoribosyl transferases that is functional in the absence of additional regulatory subunits, the structure of the regulatory HisZ subunit is distantly related to class II aminoacyl-tRNA synthetases. However, neither the mode of the oligomeric subunit arrangement nor the type of histidine binding pockets is found in these structural relatives. Common ancestry of the regulatory HisZ subunit and class II aminoacyl-tRNA synthetase may reflect the balanced need of regulated amounts of a cognate amino acid (histidine) in the translation apparatus, ultimately linking amino acid biosynthesis and protein biosynthesis in terms of function, structure and evolution.


  • Organizational Affiliation
    • EMBL Hamburg Outstation, Notkestrasse 85, Building 25A, D-22603 Hamburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 221.33 kDa 
  • Atom Count: 15,636 
  • Modeled Residue Count: 1,910 
  • Deposited Residue Count: 1,932 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP PHOSPHORIBOSYLTRANSFERASE REGULATORY SUBUNIT
A, B, D
275Thermotoga maritima MSB8Mutation(s): 0 
UniProt
Find proteins for Q9X0D3 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X0D3 
Go to UniProtKB:  Q9X0D3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X0D3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP PHOSPHORIBOSYLTRANSFERASE REGULATORY SUBUNIT275Thermotoga maritima MSB8Mutation(s): 0 
UniProt
Find proteins for Q9X0D3 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X0D3 
Go to UniProtKB:  Q9X0D3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X0D3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP PHOSPHORIBOSYLTRANSFERASE
E, F, G
208Thermotoga maritima MSB8Mutation(s): 0 
EC: 2.4.2.17
UniProt
Find proteins for Q9X0D2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X0D2 
Go to UniProtKB:  Q9X0D2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X0D2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP PHOSPHORIBOSYLTRANSFERASE208Thermotoga maritima MSB8Mutation(s): 0 
EC: 2.4.2.17
UniProt
Find proteins for Q9X0D2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X0D2 
Go to UniProtKB:  Q9X0D2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X0D2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HIS

Query on HIS



Download:Ideal Coordinates CCD File
I [auth C]
J [auth D]
M [auth E]
N [auth E]
P [auth F]
I [auth C],
J [auth D],
M [auth E],
N [auth E],
P [auth F],
S [auth G],
U [auth H],
V [auth H]
HISTIDINE
C6 H10 N3 O2
HNDVDQJCIGZPNO-YFKPBYRVSA-O
PO4

Query on PO4



Download:Ideal Coordinates CCD File
K [auth E]
L [auth E]
O [auth F]
Q [auth G]
R [auth G]
K [auth E],
L [auth E],
O [auth F],
Q [auth G],
R [auth G],
T [auth H]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free:  0.287 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.58α = 90
b = 134.403β = 90
c = 154.206γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2013-12-25
    Changes: Atomic model, Derived calculations, Other
  • Version 1.3: 2014-09-10
    Changes: Database references, Other
  • Version 1.4: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary