4DAO

Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in complex with adenine

DOI: 10.2210/pdb4DAO/pdb

Classification: TRANSFERASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-01-13 Released: 2012-09-26
Deposition Author(s): Giuseppe, P.O., Martins, N.H., Meza, A.N., Murakami, M.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free: 0.208
R-Value Work: 0.148
R-Value Observed: 0.151

wwPDB Validation 3D Report Full Report

Literature

Insights into phosphate cooperativity and influence of substrate modifications on binding and catalysis of hexameric purine nucleoside phosphorylases.

de Giuseppe, P.O., Martins, N.H., Meza, A.N., Dos Santos, C.R., Pereira, H.D., Murakami, M.T.

(2012) PLoS One 7: e44282-e44282

PubMed: 22957058 Search on PubMedSearch on PubMed Central
DOI: 10.1371/journal.pone.0044282
Primary Citation of Related Structures:
4D9H, 4D8X, 4D8Y, 4D8V, 4D98, 4DA0, 4DAN, 4DAO, 4DAB, 4DAE

PubMed Abstract:

The hexameric purine nucleoside phosphorylase from Bacillus subtilis (BsPNP233) displays great potential to produce nucleoside analogues in industry and can be exploited in the development of new anti-tumor gene therapies. In order to provide structural basis for enzyme and substrates rational optimization, aiming at those applications, the present work shows a thorough and detailed structural description of the binding mode of substrates and nucleoside analogues to the active site of the hexameric BsPNP233. Here we report the crystal structure of BsPNP233 in the apo form and in complex with 11 ligands, including clinically relevant compounds. The crystal structure of six ligands (adenine, 2'deoxyguanosine, aciclovir, ganciclovir, 8-bromoguanosine, 6-chloroguanosine) in complex with a hexameric PNP are presented for the first time. Our data showed that free bases adopt alternative conformations in the BsPNP233 active site and indicated that binding of the co-substrate (2'deoxy)ribose 1-phosphate might contribute for stabilizing the bases in a favorable orientation for catalysis. The BsPNP233-adenosine complex revealed that a hydrogen bond between the 5' hydroxyl group of adenosine and Arg(43*) side chain contributes for the ribosyl radical to adopt an unusual C3'-endo conformation. The structures with 6-chloroguanosine and 8-bromoguanosine pointed out that the Cl(6) and Br(8) substrate modifications seem to be detrimental for catalysis and can be explored in the design of inhibitors for hexameric PNPs from pathogens. Our data also corroborated the competitive inhibition mechanism of hexameric PNPs by tubercidin and suggested that the acyclic nucleoside ganciclovir is a better inhibitor for hexameric PNPs than aciclovir. Furthermore, comparative structural analyses indicated that the replacement of Ser(90) by a threonine in the B. cereus hexameric adenosine phosphorylase (Thr(91)) is responsible for the lack of negative cooperativity of phosphate binding in this enzyme.

Organizational Affiliation:

Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase deoD-type	A, B	253	Bacillus subtilis	Mutation(s): 0 Gene Names: BSU19630, deoD, punB EC: 2.4.2.1
Find proteins for O34925 (Bacillus subtilis (strain 168)) Explore O34925 Go to UniProtKB: O34925
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADE Query on ADE Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain D [B] MOL2 format, chain C [A] MOL2 format, chain D [B]	A, B	ADENINE C₅ H₅ N₅ GFFGJBXGBJISGV-UHFFFAOYSA-N		Ligand Interaction
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [B] MOL2 format, chain E [B]	B	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction