9KPY | pdb_00009kpy

Structure of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter spp. with the expression tag bound in the substrate binding site of a neighbouring molecule at 2.20 A resolution.

PDB DOI: https://doi.org/10.2210/pdb9KPY/pdb
Entry: 9KPY supersedes: 8I8J

Classification: TRANSFERASE
Organism(s): Enterobacter sp. 638
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-11-24 Released: 2024-12-11
Deposition Author(s): Ahmad, N., Sharma, P., Sharma, S., Singh, T.P.
Funding Organization(s): Indian Council of Medical Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.267 (Depositor), 0.286 (DCC)
R-Value Work:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Protein-tags and their fragments as potent inhibitors of enzymes: Structure of the ternary complex of phosphopantetheine adenylyltransferase from Enterobacter spp. with tag-peptides and phosphonoacetic acid at 2.20 angstrom resolution.

Ahmad, N., Kumar, V., Goel, V.K., Sharma, P., Sharma, S., Singh, T.P.

(2025) Protein Sci 34: e70216-e70216

PubMed: 40689715 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.70216
Primary Citation Related Structures:
9KPY

PubMed Abstract:
Phosphopantetheine adenylyltransferase (PPAT) catalyzes the penultimate step of coenzyme A (CoA) biosynthesis pathway by transferring the adenylyl group from adenosine triphosphate (ATP) to 4'-phosphopantetheine (PNS), yielding 3'-dephosphocoenzyme A and pyrophosphate. In this study, the recombinant PPAT from Enterobacter spp. strain 638 (EbPPAT) was purified and co-crystallized with phosphonoacetic acid (PAE). The structure showed the presence of three homodimers AB, CD, and EF in the asymmetric unit. The 14 extra N-terminal residues (Met-14 to Ser-1, 14-mer peptide) from the expression tag were observed in Molecules B and F. These tag-peptides occupied the PNS-binding sites of adjacent Molecules A and E, respectively. Additionally, a heptapeptide (Met-14 to Gly-8) was also observed in the PNS-binding site of Molecule C. Furthermore, two PAE molecules were present in the ATP-binding sites of Molecules B, D, and F, whereas a single PAE molecule was found in Molecules A, C, and E. This showed that tag-peptides blocked the PNS-binding site while PAE blocked the ATP-binding sites. Three peptides of the tag, including 14-mer (Met-14 to Ser-1), heptapeptide (Met-14 to Gly-8) and pentapeptide (Met-14 to Thr-10) were synthesized, and their binding affinities were estimated, which showed the K _D values of 5.5 × 10 ^-5, 1.8 × 10 ^-8, and 7.3 × 10 ^-9 M, respectively. PAE molecules bound to EbPPAT in the ATP-binding sites with a K _D of 4.77 × 10 ^-4 M. This is the first structure of PPAT with peptides bound in the substrate-binding sites, indicating a novel approach to design peptide inhibitors.

Organizational Affiliation

Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.

Macromolecule Content

Total Structure Weight: 117.24 kDa
Atom Count: 8,407
Modeled Residue Count: 989
Deposited Residue Count: 1,045
Unique protein chains: 2

Macromolecules

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| 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	173	Enterobacter sp. 638	Mutation(s): 0 Gene Names: coaD, Ent638_0105 EC: 2.7.7.3
UniProt
Find proteins for A4W515 (Enterobacter sp. (strain 638)) Explore A4W515 Go to UniProtKB: A4W515
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4W515
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heptapeptide	G [auth H]	7	Enterobacter sp. 638	Mutation(s): 0 Gene Names: coaD, Ent638_0105

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PAE (Subject of Investigation/LOI) Query on PAE Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain P [auth E] SDF format, chain Q [auth F] SDF format, chain R [auth F] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth F] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain R [auth F]	H [auth A] J [auth B] K [auth B] L [auth C] M [auth D] H [auth A], J [auth B], K [auth B], L [auth C], M [auth D], N [auth D], O [auth D], P [auth E], Q [auth F], R [auth F]	PHOSPHONOACETIC ACID C₂ H₅ O₅ P XUYJLQHKOGNDPB-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]