1QPR | pdb_00001qpr

QUINOLINATE PHOSPHORIBOSYLTRANSFERASE (QAPRTASE) FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH PHTHALATE AND PRPCP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.251 (Depositor) 
  • R-Value Work: 
    0.186 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1QPR

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Crystal structure of quinolinic acid phosphoribosyltransferase from Mycobacterium tuberculosis: a potential TB drug target.

Sharma, V.Grubmeyer, C.Sacchettini, J.C.

(1998) Structure 6: 1587-1599

  • DOI: https://doi.org/10.1016/s0969-2126(98)00156-7
  • Primary Citation Related Structures: 
    1QPN, 1QPO, 1QPQ, 1QPR

  • PubMed Abstract: 

    . Mycobacterium tuberculosis is the single most deadly human pathogen and is responsible for nearly three million deaths every year. Recent elucidation of the mode of action of isoniazid, a frontline antimycobacterial drug, suggests that NAD metabolism is extremely critical for this microorganism. M. tuberculosis depends solely on the de novo pathway to meet its NAD demand. Quinolinic acid phosphoribosyltransferase (QAPRTase), a key enzyme in the de novo biosynthesis of NAD, provides an attractive target for designing novel antitubercular drugs. . The X-ray crystal structure of the M. tuberculosis QAPRTase apoenzyme has been determined by multiple isomorphous replacement at 2.4 A resolution. Structures of the enzyme have also been solved in complex with the substrate quinolinic acid (QA), the inhibitory QA analog phthalic acid (PA), the product nicotinate mononucleotide (NAMN), and as a ternary complex with PA and a substrate analog, 5-phosphoribosyl-1-(beta-methylene)pyrophosphate (PRPCP). The structure of the nonproductive QAPRTase-PA-PRPCP Michaelis complex reveals a 5-phosphoribosyl-1-pyrophosphate-binding site that is different from the one observed in type I phosphoribosyltransferases (PRTases). The type II PRTase active site of QAPRTase undergoes conformational changes that appear to be important in determining substrate specificity and eliciting productive catalysis. . QAPRTase is the only known representative of the type II PRTase fold, an unusual alpha/beta barrel, and appears to represent convergent evolution for PRTase catalysis. The active site of type II PRTase bears little resemblance to the better known type I enzymes.


  • Organizational Affiliation
    • Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.

Macromolecule Content 

  • Total Structure Weight: 183.09 kDa 
  • Atom Count: 13,125 
  • Modeled Residue Count: 1,704 
  • Deposited Residue Count: 1,704 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
QUINOLINIC ACID PHOSPHORIBOSYLTRANSFERASE
A, B, C, D, E
A, B, C, D, E, F
284Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: NADC
EC: 2.4.2.19
UniProt
Find proteins for P9WJJ7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WJJ7 
Go to UniProtKB:  P9WJJ7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WJJ7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PPC

Query on PPC



Download:Ideal Coordinates CCD File
DA [auth F]
J [auth A]
N [auth B]
R [auth C]
U [auth D]
DA [auth F],
J [auth A],
N [auth B],
R [auth C],
U [auth D],
Z [auth E]
1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-alpha-D-ribofuranose
C6 H15 O13 P3
JFMKBQDEISBIPL-KVTDHHQDSA-N
PHT

Query on PHT



Download:Ideal Coordinates CCD File
CA [auth F]
I [auth A]
M [auth B]
Q [auth C]
V [auth D]
CA [auth F],
I [auth A],
M [auth B],
Q [auth C],
V [auth D],
Y [auth E]
PHTHALIC ACID
C8 H6 O4
XNGIFLGASWRNHJ-UHFFFAOYSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
AA [auth F]
BA [auth F]
G [auth A]
H [auth A]
K [auth B]
AA [auth F],
BA [auth F],
G [auth A],
H [auth A],
K [auth B],
L [auth B],
O [auth C],
P [auth C],
S [auth D],
T [auth D],
W [auth E],
X [auth E]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.251 (Depositor) 
  • R-Value Work:  0.186 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.448α = 90
b = 100.448β = 90
c = 145.792γ = 120
Software Package:
Software NamePurpose
PHASESphasing
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-10-21
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Structure summary