3UC5

Phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis complexed with ATP

PDB DOI: https://doi.org/10.2210/pdb3UC5/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-10-26 Released: 2012-11-07
Deposition Author(s): Timofeev, V.I., Smirnova, E.A., Chupova, L.A., Esipov, R.S., Kuranova, I.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.222
R-Value Work: 0.177
R-Value Observed: 0.179

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

X-ray study of the conformational changes in the molecule of phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis during the catalyzed reaction.

Timofeev, V., Smirnova, E., Chupova, L., Esipov, R., Kuranova, I.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1660-1670

PubMed: 23151631 Search on PubMed
DOI: https://doi.org/10.1107/S0907444912040206
Primary Citation of Related Structures:
3UC5, 4E1A

PubMed Abstract:
Structures of recombinant phosphopantetheine adenylyltransferase (PPAT) from Mycobacterium tuberculosis (PPATMt) in the apo form and in complex with the substrate ATP were determined at 1.62 and 1.70 Å resolution, respectively, using crystals grown in microgravity by the counter-diffusion method. The ATP molecule of the PPATMt-ATP complex was located with full occupancy in the active-site cavity. Comparison of the solved structures with previously determined structures of PPATMt complexed with the reaction product dephosphocoenzyme A (dPCoA) and the feedback inhibitor coenzyme A (CoA) was performed using superposition on C(α) atoms. The peculiarities of the arrangement of the ligands in the active-site cavity of PPATMt are described. The conformational states of the PPAT molecule in the consequent steps of the catalyzed reaction in the apo enzyme and the enzyme-substrate and enzyme-product complexes are characterized. It is shown that the binding of ATP and dPCoA induces the rearrangement of a short part of the polypeptide chain restricting the active-site cavity in the subunits of the hexameric enzyme molecule. The changes in the quaternary structure caused by this rearrangement are accompanied by a variation of the size of the inner water-filled channel which crosses the PPAT molecule along the threefold axis of the hexamer. The molecular mechanism of the observed changes is described.

Organizational Affiliation

Laboratory of X-ray Analysis Methods and Synchrotron Radiation, Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow, Russian Federation. tostars@mail.ru

Macromolecule Content

Total Structure Weight: 17.67 kDa
Atom Count: 1,309
Modelled Residue Count: 157
Deposited Residue Count: 157
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphopantetheine adenylyltransferase	A	157	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: coaD, kdtB, Rv2965c, MT3043, MTCY349.22, u0002e EC: 2.7.7.3
UniProt
Find proteins for P9WPA5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPA5 Go to UniProtKB: P9WPA5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WPA5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.222
R-Value Work: 0.177
R-Value Observed: 0.179
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.909	α = 90
b = 99.909	β = 90
c = 114.419	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-11-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-11-07
Type: Initial release
Version 1.1: 2012-11-28
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description