4DLK | pdb_00004dlk

Crystal Structure of ATP-Ca++ complex of purK: N5-carboxyaminoimidazole ribonucleotide synthetase

PDB DOI: https://doi.org/10.2210/pdb4DLK/pdb

Classification: LYASE
Organism(s): Bacillus anthracis str. A0248
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-02-06 Released: 2013-02-06
Deposition Author(s): Fung, L.W., Tuntland, M.L., Santarsiero, B.D., Johnson, M.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free:
0.235 (Depositor), 0.233 (DCC)
R-Value Work:
0.198 (Depositor), 0.196 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Elucidation of the bicarbonate binding site and insights into the carboxylation mechanism of (N(5))-carboxyaminoimidazole ribonucleotide synthase (PurK) from Bacillus anthracis.

Tuntland, M.L., Santarsiero, B.D., Johnson, M.E., Fung, L.W.

(2014) Acta Crystallogr D Biol Crystallogr 70: 3057-3065

PubMed: 25372694 Search on PubMed
DOI: https://doi.org/10.1107/S1399004714021166
Primary Citation Related Structures:
3QFF, 3R5H, 3V4S, 4DLK

PubMed Abstract:
Structures of (N(5))-carboxyaminoimidazole ribonucleotide synthase (PurK) from Bacillus anthracis with various combinations of ATP, ADP, Mg(2+), bicarbonate and aminoimidazole ribonucleotide (AIR) in the active site are presented. The binding site of bicarbonate has only been speculated upon previously, but is shown here for the first time. The binding involves interactions with the conserved residues Arg272, His274 and Lys348. These structures provide insights into each ligand in the active site and allow a possible mechanism to be proposed for the reaction that converts bicarbonate and AIR, in the presence of ATP, to produce (N(5))-carboxyaminoimidazole ribonucleotide. The formation of a carboxyphosphate intermediate through ATP phosphoryl transfer is proposed, followed by carboxylation of AIR to give the product, facilitated by a cluster of conserved residues and an active-site water network.

Organizational Affiliation

Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA.

Macromolecule Content

Total Structure Weight: 86.77 kDa
Atom Count: 6,368
Modeled Residue Count: 760
Deposited Residue Count: 760
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylaminoimidazole carboxylase, ATPase subunit	A, B	380	Bacillus anthracis str. A0248	Mutation(s): 0 Gene Names: BAS0276, BA_0289, GBAA_0289, purK EC: 4.1.1.21 (PDB Primary Data), 6.3.4.18 (UniProt)
UniProt
Find proteins for A0A6L8P0X7 (Bacillus anthracis) Explore A0A6L8P0X7 Go to UniProtKB: A0A6L8P0X7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6L8P0X7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B]	F [auth A], G [auth A], H [auth A], L [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	C [auth A], D [auth A], E [auth A], J [auth B], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.235 (Depositor), 0.233 (DCC)
R-Value Work: 0.198 (Depositor), 0.196 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.368	α = 90
b = 84.476	β = 90
c = 167.269	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-02-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-02-06
Type: Initial release
Version 1.1: 2014-11-12
Changes: Database references
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations