1QJC

Phosphopantetheine Adenylyltransferase from Escherichia coli in complex with 4'-phosphopantetheine

PDB DOI: https://doi.org/10.2210/pdb1QJC/pdb

Classification: COENZYME A BIOSYNTHESIS
Organism(s): Escherichia coli
Mutation(s): No

Deposited: 1999-06-23 Released: 2001-06-27
Deposition Author(s): Izard, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.247
R-Value Work: 0.216
R-Value Observed: 0.216

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The Crystal Structures of Phosphopantetheine Adenylyltransferase with Bound Substrates Reveal the Enzyme'S Catalytic Mechanism

Izard, T.

(2001) J Mol Biol 315: 487

PubMed: 11812124 Search on PubMed
DOI: https://doi.org/10.1006/jmbi.2001.5272
Primary Citation of Related Structures:
1GN8, 1QJC

PubMed Abstract:
Phosphopantetheine adenylyltransferase (PPAT) is an essential enzyme in the coenzyme A pathway that catalyzes the reversible transfer of an adenylyl group from ATP to 4'-phosphopantetheine (Ppant) in the presence of magnesium. To investigate the reaction mechanism, the high-resolution crystal structures of the Escherichia coli PPAT have been determined in the presence of either ATP or Ppant. Structural details of the catalytic center revealed specific roles for individual amino acid residues involved in substrate binding and catalysis. The side-chain of His18 stabilizes the expected pentacovalent intermediate, whereas the side-chains of Thr10 and Lys42 orient the nucleophile for an in-line displacement mechanism. The binding site for the manganese ion that interacts with the phosphate groups of the nucleotide has also been identified. Within the PPAT hexamer, one trimer is in its substrate-free state, whereas the other is in a substrate-bound state.

Organizational Affiliation

Department of Structural Biology, St. Jude Children's Research Hospital, 332 North Lauderdale Street, Memphis, TN 38105-2794, USA. Tina.Izard@stjude.org

Macromolecule Content

Total Structure Weight: 36.3 kDa
Atom Count: 2,796
Modelled Residue Count: 314
Deposited Residue Count: 316
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, B	158	Escherichia coli	Mutation(s): 0 EC: 2.7.7.3
UniProt
Find proteins for P0A6I6 (Escherichia coli (strain K12)) Explore P0A6I6 Go to UniProtKB: P0A6I6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A6I6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PNS Query on PNS Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	4'-PHOSPHOPANTETHEINE C₁₁ H₂₃ N₂ O₇ P S JDMUPRLRUUMCTL-VIFPVBQESA-N		Interactions Focus chain H [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B]	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B]