4YB7 | pdb_00004yb7

Adenosine triphosphate phosphoribosyltransferase from Campylobacter jejuni in complex with ATP

PDB DOI: https://doi.org/10.2210/pdb4YB7/pdb

Classification: TRANSFERASE
Organism(s): Campylobacter jejuni RM1221
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-02-18 Released: 2016-03-09
Deposition Author(s): Mittelstaedt, G., Moggre, G.-J., Parker, E.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.254 (Depositor), 0.258 (DCC)
R-Value Work:
0.231 (Depositor), 0.235 (DCC)
R-Value Observed:
0.232 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Campylobacter jejuni adenosine triphosphate phosphoribosyltransferase is an active hexamer that is allosterically controlled by the twisting of a regulatory tail.

Mittelstadt, G., Moggre, G.J., Panjikar, S., Nazmi, A.R., Parker, E.J.

(2016) Protein Sci 25: 1492-1506

PubMed: 27191057 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.2948
Primary Citation Related Structures:
4YB5, 4YB6, 4YB7

PubMed Abstract:
Adenosine triphosphate phosphoribosyltransferase (ATP-PRT) catalyzes the first committed step of the histidine biosynthesis in plants and microorganisms. Here, we present the functional and structural characterization of the ATP-PRT from the pathogenic ε-proteobacteria Campylobacter jejuni (CjeATP-PRT). This enzyme is a member of the long form (HisGL ) ATP-PRT and is allosterically inhibited by histidine, which binds to a remote regulatory domain, and competitively inhibited by AMP. In the crystalline form, CjeATP-PRT was found to adopt two distinctly different hexameric conformations, with an open homohexameric structure observed in the presence of substrate ATP, and a more compact closed form present when inhibitor histidine is bound. CjeATP-PRT was observed to adopt only a hexameric quaternary structure in solution, contradicting previous hypotheses favoring an allosteric mechanism driven by an oligomer equilibrium. Instead, this study supports the conclusion that the ATP-PRT long form hexamer is the active species; the tightening of this structure in response to remote histidine binding results in an inhibited enzyme.

Organizational Affiliation

Maurice Wilkins Centre, Biomolecular Interaction Centre, Christchurch, 8140, New Zealand.

Macromolecule Content

Total Structure Weight: 411.9 kDa
Atom Count: 26,987
Modeled Residue Count: 3,531
Deposited Residue Count: 3,600
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP phosphoribosyltransferase	A [auth B] B [auth C] C [auth D] D [auth E] E [auth I] A [auth B], B [auth C], C [auth D], D [auth E], E [auth I], F [auth K], G [auth A], H [auth F], I [auth G], J [auth H], K [auth J], L	300	Campylobacter jejuni RM1221	Mutation(s): 0 Gene Names: hisG, CJE1769 EC: 2.4.2.17
UniProt
Find proteins for Q5HSJ4 (Campylobacter jejuni (strain RM1221)) Explore Q5HSJ4 Go to UniProtKB: Q5HSJ4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5HSJ4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain CA [auth K] SDF format, chain EA [auth A] SDF format, chain GA [auth F] SDF format, chain IA [auth G] SDF format, chain KA [auth H] SDF format, chain NA [auth J] SDF format, chain QA [auth L] SDF format, chain U [auth D] SDF format, chain X [auth E] SDF format, chain S [auth C] SDF format, chain O [auth B] SDF format, chain AA [auth I] MOL2 format, chain CA [auth K] MOL2 format, chain EA [auth A] MOL2 format, chain GA [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain KA [auth H] MOL2 format, chain NA [auth J] MOL2 format, chain QA [auth L] MOL2 format, chain U [auth D] MOL2 format, chain X [auth E] MOL2 format, chain S [auth C] MOL2 format, chain O [auth B] MOL2 format, chain AA [auth I] mmCIF format, chain CA [auth K] mmCIF format, chain EA [auth A] mmCIF format, chain GA [auth F] mmCIF format, chain IA [auth G] mmCIF format, chain KA [auth H] mmCIF format, chain NA [auth J] mmCIF format, chain QA [auth L] mmCIF format, chain U [auth D] mmCIF format, chain X [auth E] mmCIF format, chain S [auth C] mmCIF format, chain O [auth B] mmCIF format, chain AA [auth I]	AA [auth I] CA [auth K] EA [auth A] GA [auth F] IA [auth G] AA [auth I], CA [auth K], EA [auth A], GA [auth F], IA [auth G], KA [auth H], NA [auth J], O [auth B], QA [auth L], S [auth C], U [auth D], X [auth E]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain AA [auth I] Focus chain CA [auth K] Focus chain EA [auth A] Focus chain GA [auth F] Focus chain IA [auth G] Focus chain KA [auth H] Focus chain NA [auth J] Focus chain O [auth B] Focus chain QA [auth L] Focus chain S [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth I] Focus chain CA [auth K] Focus chain EA [auth A] Focus chain GA [auth F] Focus chain IA [auth G] Focus chain KA [auth H] Focus chain NA [auth J] Focus chain O [auth B] Focus chain QA [auth L] Focus chain S [auth C] Focus chain U [auth D] Focus chain X [auth E]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain MA [auth J] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain Z [auth I] SDF format, chain W [auth E] MOL2 format, chain MA [auth J] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain Z [auth I] MOL2 format, chain W [auth E] mmCIF format, chain MA [auth J] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain Z [auth I] mmCIF format, chain W [auth E]	MA [auth J] N [auth B] Q [auth C] R [auth C] W [auth E] MA [auth J], N [auth B], Q [auth C], R [auth C], W [auth E], Z [auth I]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain MA [auth J] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain W [auth E] Focus chain Z [auth I] Interactions & Density Focus chain MA [auth J] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain W [auth E] Focus chain Z [auth I]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain OA [auth J] MOL2 format, chain OA [auth J] mmCIF format, chain OA [auth J]	OA [auth J]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain OA [auth J] Interactions & Density Focus chain OA [auth J]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain BA [auth K] SDF format, chain FA [auth F] SDF format, chain HA [auth G] SDF format, chain JA [auth H] SDF format, chain LA [auth J] SDF format, chain M [auth B] SDF format, chain PA [auth L] SDF format, chain Y [auth I] SDF format, chain V [auth E] SDF format, chain T [auth D] SDF format, chain P [auth C] SDF format, chain DA [auth A] MOL2 format, chain BA [auth K] MOL2 format, chain FA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain JA [auth H] MOL2 format, chain LA [auth J] MOL2 format, chain M [auth B] MOL2 format, chain PA [auth L] MOL2 format, chain Y [auth I] MOL2 format, chain V [auth E] MOL2 format, chain T [auth D] MOL2 format, chain P [auth C] MOL2 format, chain DA [auth A] mmCIF format, chain BA [auth K] mmCIF format, chain FA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain JA [auth H] mmCIF format, chain LA [auth J] mmCIF format, chain M [auth B] mmCIF format, chain PA [auth L] mmCIF format, chain Y [auth I] mmCIF format, chain V [auth E] mmCIF format, chain T [auth D] mmCIF format, chain P [auth C] mmCIF format, chain DA [auth A]	BA [auth K] DA [auth A] FA [auth F] HA [auth G] JA [auth H] BA [auth K], DA [auth A], FA [auth F], HA [auth G], JA [auth H], LA [auth J], M [auth B], P [auth C], PA [auth L], T [auth D], V [auth E], Y [auth I]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth K] Focus chain DA [auth A] Focus chain FA [auth F] Focus chain HA [auth G] Focus chain JA [auth H] Focus chain LA [auth J] Focus chain M [auth B] Focus chain P [auth C] Focus chain PA [auth L] Focus chain T [auth D] Focus chain V [auth E] Focus chain Y [auth I] Interactions & Density Focus chain BA [auth K] Focus chain DA [auth A] Focus chain FA [auth F] Focus chain HA [auth G] Focus chain JA [auth H] Focus chain LA [auth J] Focus chain M [auth B] Focus chain P [auth C] Focus chain PA [auth L] Focus chain T [auth D] Focus chain V [auth E] Focus chain Y [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.254 (Depositor), 0.258 (DCC)
R-Value Work: 0.231 (Depositor), 0.235 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.667	α = 101.11
b = 91.835	β = 95.21
c = 154.903	γ = 118.14

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-03-09

Deposition Author(s):

Mittelstaedt, G.

Moggre, G.-J.

Parker, E.J.

Revision History (Full details and data files)

Version 1.0: 2016-03-09
Type: Initial release
Version 1.1: 2018-09-05
Changes: Advisory, Data collection, Database references, Derived calculations
Version 1.2: 2024-10-23
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description, Structure summary