Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 A resolution

Journal Article · Mon Nov 01 00:00:00 EDT 2010 · Proteins: Structure, Function, Bioinformatics

DOI:https://doi.org/10.1002/prot.22829· OSTI ID:1014327

Sampathkumar, P; Swaminathan, S; Lu, F; Zhao, X; Li, Z; Gilmore, J; Bain, K; Rutter, M E; Gheyi, T; Schwinn, D; Bonanno, J B; Pieper, U; Fajardo, J E; Fiser, A; Almo, S C; Chance, M R; Baker, D; Atwell, S; Thompson, D A; Emtage, J S ; Wasserman, S R; Sali, A; Sauder, J M; Burley, S K

Gram-negative bacteria typically overcome poor permeability of outer membranes through general porins like OmpF and OmpC, which form water-filled transmembrane pores permitting diffusion of hydrophilic molecules with no particular selectivity. Many bacteria lacking such general porins use substrate-specific porins to overcome growth-limiting conditions and facilitate selective transport of metabolites. Exclusive reliance on substrate-specific porins yields lower membrane permeability to small molecules (<600 Da) versus that seen for Escherichia coli. In Pseudomonads, transit of most small molecules across the cell membrane is thought to be mediated by substrate-specific channels of the OprD superfamily. This property explains, at least in part, the high incidence of Pseudomonas aeruginosa antibiotic resistance. High-throughput DNA sequencing of the P. aeruginosa chromosome revealed the presence of 19 genes encoding structurally related, substrate-specific porins (with 30-45% pairwise amino acid sequence identity) that mediate transmembrane passage of small, water-soluble compounds. The OprD superfamily encompasses the eponymous OprD subfamily, which includes 9 P. aeruginosa proteins that convey basic amino acids and carbapenem antibiotics, and the OpdK subfamily, which includes 11 P. aeruginosa proteins that convey aromatic acids and other small aromatic compounds. Genome sequencing of other gram-negative bacteria has revealed additional members of the OprD and OpdK subfamilies in various organisms, including other pseudomonads. Among the many bacteria in which OprD superfamily members have been identified are P. putida, P. fluorescens Pf-5, P. syringae, and Azotobacter vinelandii, all of which share closely related genes that encode the so-called BenF-like porins. In P. putida, benF is part of an operon involved in benzoate catabolism regulated by benR. Within this operon, benK, benE, and benF genes have been suggested to contribute toward either influx or efflux of benzoate. BLAST analysis of the amino acid sequence of P. fluorescens Pf-5 gene PFL1329 (Uniprot id: http://www.uniprot.org/uniprot/Q4KH25) against P. putida KT2440 strain identified 20 related porins. The top six hits include P. putida KT2440 genes PP1383 (annotated as BenF-like), PP2517 (annotated as BenF-like), and PP3168 (annotated as BenF), which share sequence identities of 76%, 66%, and 44% with PFL1329, respectively. The precise functions of these genes are not yet known. Therefore, we refer to the protein product of gene PFL1329 as PflBenF-like, which reflects its current annotation in the Uniprot database. Crystal structures of OprD and OpdK (vanillate specific porin), both from P. aeruginosa (designated below as PaOprD and PaOpdK, respectively) have been determined. Herein, we report the crystal structure of a putative BenF-like porin from P. fluorescens Pf-5 (PflBenF-like). For the sake of brevity, all subsequent references to the PflBenF-like porin will be made using PflBenF. X-ray crystallography revealed a canonical 18-stranded {beta}-barrel fold that forms a central pore with a diameter of {approx}4.6 E. We describe detailed comparisons of the PflBenF structure with those of PaOprD and PaOpdK.

• Research Organization: Brookhaven National Lab. (BNL), Upton, NY (United States)
• Sponsoring Organization: ELI LILLY & COMPANY
• DOE Contract Number: DE-AC02-98CH10886
• OSTI ID: 1014327
• Report Number(s): BNL-93987-2010-JA; 600301010; TRN: US201111%%280
• Journal Information: Proteins: Structure, Function, Bioinformatics, Vol. 78, Issue 14; ISSN 0887-3585
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
AMINO ACID SEQUENCE
AMINO ACIDS
ANTIBIOTICS
AROMATICS
AZOTOBACTER
BACTERIA
CARBOXYLIC ACIDS
CATABOLISM
CELL MEMBRANES
CHROMOSOMES
CRYSTAL STRUCTURE
CRYSTALLOGRAPHY
DNA SEQUENCING
ESCHERICHIA COLI
GENES
METABOLITES
PORINS
PROTEINS
PSEUDOMONAS
RESOLUTION
BenF-like
substrate-specific porin
OprD superfamily
OprD subfamily
OpdK subfamily
benzoate
Pseudomonas
integral membrane protein