3X1K

crystal structure of Phosphoapantetheine adenylyltransferase PPAT/CoaD with AMP-PNP from Pseudomonas aerugonosa

PDB DOI: https://doi.org/10.2210/pdb3X1K/pdb

Classification: TRANSFERASE
Organism(s): Pseudomonas aeruginosa 2192
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-11-20 Released: 2015-11-25
Deposition Author(s): Chatterjee, R., Datta, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.245
R-Value Work: 0.190
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Transition of phosphopantetheine adenylyltransferase from catalytic to allosteric state is characterized by ternary complex formation in Pseudomonas aeruginosa

Chatterjee, R., Mondal, A., Basu, A., Datta, S.

(2016) Biochim Biophys Acta 1864: 773-786

PubMed: 27041211 Search on PubMed
DOI: https://doi.org/10.1016/j.bbapap.2016.03.018
Primary Citation of Related Structures:
3X1J, 3X1K, 3X1M, 4RUK

PubMed Abstract:
Phosphopantetheine adenylyltransferase (PPAT) is a rate limiting enzyme which catalyzes the conversion of ATP and pantetheine to dephosphocoenzyme and pyrophosphate. The enzyme is allosteric in nature and regulated by Coenzyme A (CoA) through feedback inhibition. So far, several structures have been solved to decipher the catalytic mechanism of this enzyme.

Organizational Affiliation

Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology, 4 Raja SC Mullick Road, Jadavpur, Kolkata-700032, West Bengal, India. Electronic address: rakesh.2665675@gmail.com.

Macromolecule Content

Total Structure Weight: 111.71 kDa
Atom Count: 7,865
Modelled Residue Count: 944
Deposited Residue Count: 954
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphopantetheine adenylyltransferase	A, B, C, D, E A, B, C, D, E, F	159	Pseudomonas aeruginosa 2192	Mutation(s): 0 Gene Names: coaD, PA0363, PA2G_04277 EC: 2.7.7.3
UniProt
Find proteins for A0A0X1KGP2 (Pseudomonas aeruginosa 2192) Explore A0A0X1KGP2 Go to UniProtKB: A0A0X1KGP2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0X1KGP2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain EA [auth E] SDF format, chain G [auth A] SDF format, chain KA [auth F] SDF format, chain L [auth B] SDF format, chain T [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain L [auth B] MOL2 format, chain T [auth C]	AA [auth D] EA [auth E] G [auth A] KA [auth F] L [auth B] AA [auth D], EA [auth E], G [auth A], KA [auth F], L [auth B], T [auth C]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain AA [auth D] Focus chain EA [auth E] Focus chain G [auth A] Focus chain KA [auth F] Focus chain L [auth B] Focus chain T [auth C] Interactions & Density Focus chain AA [auth D] Focus chain EA [auth E] Focus chain G [auth A] Focus chain KA [auth F] Focus chain L [auth B] Focus chain T [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain V [auth C] MOL2 format, chain J [auth A] MOL2 format, chain V [auth C]	J [auth A], V [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain J [auth A] Focus chain V [auth C] Interactions & Density Focus chain J [auth A] Focus chain V [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C]	W [auth C], X [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain W [auth C] Focus chain X [auth C]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain FA [auth E] SDF format, chain BA [auth D] SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain GA [auth E] SDF format, chain H [auth A] SDF format, chain HA [auth E] SDF format, chain IA [auth F] SDF format, chain JA [auth F] SDF format, chain K [auth A] SDF format, chain LA [auth F] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain P [auth B] SDF format, chain U [auth C] SDF format, chain Y [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain GA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth E] MOL2 format, chain IA [auth F] MOL2 format, chain JA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D]	BA [auth D] CA [auth E] DA [auth E] FA [auth E] GA [auth E] BA [auth D], CA [auth E], DA [auth E], FA [auth E], GA [auth E], H [auth A], HA [auth E], IA [auth F], JA [auth F], K [auth A], LA [auth F], M [auth B], N [auth B], P [auth B], U [auth C], Y [auth D]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain H [auth A] Focus chain HA [auth E] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain K [auth A] Focus chain LA [auth F] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain Y [auth D] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain H [auth A] Focus chain HA [auth E] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain K [auth A] Focus chain LA [auth F] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain Y [auth D]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain Z [auth D] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain Z [auth D]	I [auth A] O [auth B] Q [auth B] R [auth B] S [auth B] I [auth A], O [auth B], Q [auth B], R [auth B], S [auth B], Z [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain O [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain Z [auth D] Interactions & Density Focus chain I [auth A] Focus chain O [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.245
R-Value Work: 0.190
R-Value Observed: 0.193
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.325	α = 90
b = 89.787	β = 98.27
c = 80.315	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-11-25

Deposition Author(s):

Chatterjee, R.

Datta, S.

Revision History (Full details and data files)

Version 1.0: 2015-11-25
Type: Initial release
Version 1.1: 2016-04-20
Changes: Data collection
Version 1.2: 2016-05-04
Changes: Database references
Version 1.3: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description