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The Gram-negative porin 1 (GBP-1) Family [Function: Non-specific diffusion channels] Seed alignment | Full alignment | Pfam page | Pfam Wiki page | TC-DB page

This family consists of the general diffusion porins from mainly the Beta and Gamma subdivisions of Proteobacteria. Although the porins of this family share common structural and functional properties with the porins of General Bacterial Porin Family 2 (GBP-2) and the Rhodobacter porin family, their sequence similarity is rather low. The porins form large aqueous channels, facilitating the diffusion of small hydrophilic molecules through the outer membrane in a non-specific manner. Important aspects of the channel activity are the conductance, the voltage dependence and the pH sensitivity. Several porins of this family have been determined at low resolution (Omp32, OmpF, Phosphoporin, OmpK36) suggesting that the 16-stranded ß-barrel is a common structural feature. In addition to that, the porins of this family seem to require trimerization in order to function properly. In Providencia stuartii, these porins form primitive junctions between P. stuartii cells. These junctions could foster the formation of floating communities and support intercellular communications.


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Literature references


Outer Membrane Proteins OmpA, FhuA, OmpF, EstA, BtuB, and OmpX Have Unique Lipopolysaccharide Fingerprints
J Chem Theory Comput. 2019 Apr 9;15(4):2608-2619. doi: 10.1021/acs.jctc.8b01059. Epub 2019 Mar 21.
PMID: 30848905

Lipid Headgroup Charge and Acyl Chain Composition Modulate Closure of Bacterial ß-Barrel Channels
Int J Mol Sci. 2019 Feb 5;20(3):674. doi: 10.3390/ijms20030674.
PMID: 30764475

Getting Drugs into Gram-Negative Bacteria: Rational Rules for Permeation through General Porins
ACS Infect Dis. 2018 Oct 12;4(10):1487-1498. doi: 10.1021/acsinfecdis.8b00108. Epub 2018 Aug 17.
PMID: 29962203

Porin self-association enables cell-to-cell contact in Providencia stuartii floating communities
Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):E2220-E2228. doi: 10.1073/pnas.1714582115. Epub 2018 Feb 23.
PMID: 29476011

Influence of the surrounding environment in re-naturalized ß-barrel membrane proteins
Biophys Chem. 2018 Mar;234:6-15. doi: 10.1016/j.bpc.2017.12.003. Epub 2018 Jan 2.
PMID: 29306652

A New Strain Collection for Improved Expression of Outer Membrane Proteins
Front Cell Infect Microbiol. 2017 Nov 7;7:464. doi: 10.3389/fcimb.2017.00464. eCollection 2017.
PMID: 29164072

Engineering a Novel Porin OmpGF Via Strand Replacement from Computational Analysis of Sequence Motif
Biochim Biophys Acta Biomembr. 2017 Jul;1859(7):1180-1189. doi: 10.1016/j.bbamem.2017.03.012. Epub 2017 Mar 21.
PMID: 28341438

Deducing the symmetry of helical assemblies: Applications to membrane proteins
J Struct Biol. 2016 Aug;195(2):167-178. doi: 10.1016/j.jsb.2016.05.011. Epub 2016 May 30.
PMID: 27255388

Magnetically Directed Two-Dimensional Crystallization of OmpF Membrane Proteins in Block Copolymers
J Am Chem Soc. 2016 Jan 13;138(1):28-31. doi: 10.1021/jacs.5b03320. Epub 2015 Dec 24.
PMID: 26677866

Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations
J Gen Physiol. 2013 Oct;142(4):465-75. doi: 10.1085/jgp.201311014.
PMID: 24081985

Intrinsically disordered protein threads through the bacterial outer-membrane porin OmpF
Science. 2013 Jun 28;340(6140):1570-4. doi: 10.1126/science.1237864.
PMID: 23812713

Ion-channels: goals for function-oriented synthesis
Acc Chem Res. 2013 Dec 17;46(12):2773-80. doi: 10.1021/ar400007w. Epub 2013 May 7.
PMID: 23651489

Asymmetric pore occupancy in crystal structure of OmpF porin from Salmonella typhi
J Struct Biol. 2012 Jun;178(3):233-44. doi: 10.1016/j.jsb.2012.04.005. Epub 2012 Apr 16.
PMID: 22525817

Structural basis for solute transport, nucleotide regulation, and immunological recognition of Neisseria meningitidis PorB
Proc Natl Acad Sci U S A. 2010 Apr 13;107(15):6811-6. doi: 10.1073/pnas.0912115107. Epub 2010 Mar 29.
PMID: 20351243

Cation-selective pathway of OmpF porin revealed by anomalous X-ray diffraction
J Mol Biol. 2010 Feb 19;396(2):293-300. doi: 10.1016/j.jmb.2009.11.042. Epub 2009 Nov 20.
PMID: 19932117

Crystal structures of the OmpF porin: function in a colicin translocon
EMBO J. 2008 Aug 6;27(15):2171-80. doi: 10.1038/emboj.2008.137. Epub 2008 Jul 17.
PMID: 18636093

Crystal structure of osmoporin OmpC from E. coli at 2.0 A
J Mol Biol. 2006 Oct 6;362(5):933-42. doi: 10.1016/j.jmb.2006.08.002. Epub 2006 Aug 3.
PMID: 16949612

High resolution crystal structures and molecular dynamics studies reveal substrate binding in the porin Omp32
J Biol Chem. 2006 Mar 17;281(11):7413-20. doi: 10.1074/jbc.M510939200. Epub 2006 Jan 23.
PMID: 16434398

Solute uptake through general porins
Front Biosci. 2003 May 1;8:d1055-71. doi: 10.2741/1132.
PMID: 12700124

Crystal structure of Omp32, the anion-selective porin from Comamonas acidovorans, in complex with a periplasmic peptide at 2.1 A resolution
Structure. 2000 Sep 15;8(9):981-92. doi: 10.1016/s0969-2126(00)00189-1.
PMID: 10986465

Crystal structure and functional characterization of OmpK36, the osmoporin of Klebsiella pneumoniae
Structure. 1999 Apr 15;7(4):425-34. doi: 10.1016/s0969-2126(99)80055-0.
PMID: 10196126

The structure of OmpF porin in a tetragonal crystal form
Structure. 1995 Oct 15;3(10):1041-50. doi: 10.1016/s0969-2126(01)00240-4.
PMID: 8589999

Crystal structures explain functional properties of two E. coli porins
Nature. 1992 Aug 27;358(6389):727-33. doi: 10.1038/358727a0.
PMID: 1380671

The bacterial porin superfamily: sequence alignment and structure prediction
Mol Microbiol. 1991 Sep;5(9):2153-64. doi: 10.1111/j.1365-2958.1991.tb02145.x.
PMID: 1662760

Proteins in this family with 3D-structure
View Entry
Description
Organism
Length
# strands
OmpK37
Klebsiella pneumoniae
374
16
OmpC protein
Klebsiella pneumoniae
365
16
Outer membrane protein 1A/OmpK35 porin
Klebsiella aerogenes (strain ATCC 13048 / DSM 30053 / JCM 1235 / KCTC 2190/ NBRC 13534 / NCIMB 10102 / NCTC 10006) (Enterobacter aerogenes)
359
16
Outer membrane protein F
Klebsiella pneumoniae IS46
351
16
Porin 1
Providencia stuartii
374
16
Osmoporin Omp36
Klebsiella aerogenes (Enterobacter aerogenes)
375
16
OmpF porin
Enterobacter cloacae
351
16
Porin (PorB)
Neisseria gonorrhoeae
327
16
Outer membrane protein A
Neisseria meningitidis serogroup B (strain MC58)
331
16
PorA class 1 protein
Escherichia coli (strain K12)
362
16
Nucleoside-specific channel-forming protein Tsx
Salmonella typhi
378
16
Vitamin B12 transporter BtuB
Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)
375
16
Membrane protein
Escherichia coli
364
16
Ferrichrome outer membrane transporter/phage receptor
Escherichia coli (strain K12)
367
16
PorA class 1 protein
Escherichia coli (strain K12)
351
16
Vitamin B12 transporter BtuB
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
363
16
Outer membrane protein X
Klebsiella pneumoniae
363
16
Outer membrane protein II
Neisseria meningitidis
322
12
Outer membrane porin protein OmpD
Providencia stuartii
365
16
OmpC porin
Enterobacter cloacae
363
16
OmpK36
Klebsiella pneumoniae
365
16
OmpK36
Klebsiella pneumoniae
369
16
OmpK36
Klebsiella pneumoniae
367
16


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