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PDBsum entry 1e54
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Outer membrane protein PDB id
1e54

 

 

 

 

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Contents
Protein chain
332 a.a. *
Ligands
ASP-ASN-TRP-GLN-
ASN-GLY-THR-SER
SO4
Metals
_CA
Waters ×98
* Residue conservation analysis
PDB id:
1e54
Name: Outer membrane protein
Title: Anion-selective porin from comamonas acidovorans
Structure: Outer membrane porin protein 32. Chain: a. Synonym: omp32. Omp32. Chain: b
Source: Comamonas acidovorans. Organism_taxid: 80866. Atcc: 15668. Cellular_location: outer membrane. Cellular_location: outer membrane
Biol. unit: Hexamer (from PDB file)
Resolution:
2.10Å     R-factor:   0.200     R-free:   0.235
Authors: K.Zeth,K.Diederichs,W.Welte,H.Engelhardt
Key ref:
K.Zeth et al. (2000). Crystal structure of Omp32, the anion-selective porin from Comamonas acidovorans, in complex with a periplasmic peptide at 2.1 A resolution. Structure, 8, 981-992. PubMed id: 10986465 DOI: 10.1016/S0969-2126(00)00189-1
Date:
17-Jul-00     Release date:   12-Jul-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P24305  (OMP32_DELAC) -  Outer membrane porin protein 32 from Delftia acidovorans
Seq:
Struc: 		351 a.a.
332 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 

 
DOI no: 10.1016/S0969-2126(00)00189-1 Structure 8:981-992 (2000)
PubMed id: 10986465  
 
 
Crystal structure of Omp32, the anion-selective porin from Comamonas acidovorans, in complex with a periplasmic peptide at 2.1 A resolution.
K.Zeth, K.Diederichs, W.Welte, H.Engelhardt.
 
  ABSTRACT  
 
BACKGROUND: Porins provide diffusion channels for salts and small organic molecules in the outer membrane of bacteria. In OmpF from Escherichia coli and related porins, an electrostatic field across the channel and a potential, originating from a surplus of negative charges, create moderate cation selectivity. Here, we investigate the strongly anion-selective porin Omp32 from Comamonas acidovorans, which is closely homologous to the porins of pathogenic Bordetella and Neisseria species. RESULTS: The crystal structure of Omp32 was determined to a resolution of 2.1 A using single isomorphous replacement with anomalous scattering (SIRAS). The porin consists of a 16-stranded beta barrel with eight external loops and seven periplasmic turns. Loops 3 and 8, together with a protrusion located within beta-strand 2, narrow the cross-section of the pore considerably. Arginine residues create a charge filter in the constriction zone and a positive surface potential at the external and periplasmic faces. One sulfate ion was bound to Arg38 in the channel constriction zone. A peptide of 5.8 kDa appeared bound to Omp32 in a 1:1 stoichiometry on the periplasmic side close to the symmetry axis of the trimer. Eight amino acids of this peptide could be identified, revealing specific interactions with beta-strand 1 of the porin. CONCLUSIONS: The Omp32 structure explains the strong anion selectivity of this porin. Selectivity is conferred by a positive potential, which is not attenuated by negative charges inside the channel, and by an extremely narrow constriction zone. Moreover, Omp32 represents the anchor molecule for a peptide which is homologous to proteins that link the outer membrane to the cell wall peptidoglycan.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. The surface of Omp32 oriented towards the outer membrane. A girdle of ten lysine residues and one arginine is enveloped by eight visible, oppositely charged aspartate residues and one glutamate residue. The b strands are indicated in yellow. The surface was calculated using the program MSMS [51], and the representation was produced using the program DINO (http://www.bioz.unibas.ch/ not, vert, similar-xray/dino).
 
  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 981-992) copyright 2000.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21130656 V.Karuppiah, J.L.Berry, and J.P.Derrick (2011).
Outer membrane translocons: structural insights into channel formation.
  Trends Microbiol, 19, 40-48.  
21078354 W.Suginta, K.R.Mahendran, W.Chumjan, E.Hajjar, A.Schulte, M.Winterhalter, and H.Weingart (2011).
Molecular analysis of antimicrobial agent translocation through the membrane porin BpsOmp38 from an ultraresistant Burkholderia pseudomallei strain.
  Biochim Biophys Acta, 1808, 1552-1559.  
20868223 D.R.Carrillo, C.Parthier, N.Jänckel, J.Grandke, M.Stelter, S.Schilling, M.Boehme, P.Neumann, R.Wolf, H.U.Demuth, M.T.Stubbs, and J.U.Rahfeld (2010).
Kinetic and structural characterization of bacterial glutaminyl cyclases from Zymomonas mobilis and Myxococcus xanthus.
  Biol Chem, 391, 1419-1428.
PDB codes: 3nok 3nol 3nom
20836765 K.Zeth, and M.Thein (2010).
Porins in prokaryotes and eukaryotes: common themes and variations.
  Biochem J, 431, 13-22.  
20351243 M.Tanabe, C.M.Nimigean, and T.M.Iverson (2010).
Structural basis for solute transport, nucleotide regulation, and immunological recognition of Neisseria meningitidis PorB.
  Proc Natl Acad Sci U S A, 107, 6811-6816.
PDB codes: 3a2r 3a2s 3a2t 3a2u 3vzt 3vzu 3vzw
18849407 R.G.Coleman, and K.A.Sharp (2009).
Finding and characterizing tunnels in macromolecules with application to ion channels and pores.
  Biophys J, 96, 632-645.  
17932925 J.Martin, A.G.de Brevern, and A.C.Camproux (2008).
In silico local structure approach: a case study on outer membrane proteins.
  Proteins, 71, 92.  
18451061 J.S.Bennett, M.J.Callaghan, J.P.Derrick, and M.C.Maiden (2008).
Variation in the Neisseria lactamica porin, and its relationship to meningococcal PorB.
  Microbiology, 154, 1525-1534.  
18584152 T.Burghardt, M.Saller, S.Gürster, D.Müller, C.Meyer, U.Jahn, E.Hochmuth, R.Deutzmann, F.Siedler, P.Babinger, R.Wirth, H.Huber, and R.Rachel (2008).
Insight into the proteome of the hyperthermophilic Crenarchaeon Ignicoccus hospitalis: the major cytosolic and membrane proteins.
  Arch Microbiol, 190, 379-394.  
17567284 A.P.Godoy, F.C.Reis, L.F.Ferraz, M.M.Gerrits, S.Mendonça, J.G.Kusters, L.M.Ottoboni, M.L.Ribeiro, and J.Pedrazzoli (2007).
Differentially expressed genes in response to amoxicillin in Helicobacter pylori analyzed by RNA arbitrarily primed PCR.
  FEMS Immunol Med Microbiol, 50, 226-230.  
17828567 H.Engelhardt, T.Meins, M.Poynor, V.Adams, S.Nussberger, W.Welte, and K.Zeth (2007).
High-level expression, refolding and probing the natural fold of the human voltage-dependent anion channel isoforms I and II.
  J Membr Biol, 216, 93.  
17163971 T.Burghardt, D.J.Näther, B.Junglas, H.Huber, and R.Rachel (2007).
The dominating outer membrane protein of the hyperthermophilic Archaeum Ignicoccus hospitalis: a novel pore-forming complex.
  Mol Microbiol, 63, 166-176.  
16493651 M.M.Gromiha, and M.Suwa (2006).
Discrimination of outer membrane proteins using machine learning algorithms.
  Proteins, 63, 1031-1037.  
17947032 R.Jackups, and J.Liang (2006).
Combinatorial model for sequence and spatial motif discovery in short sequence fragments: examples from beta-barrel membrane proteins.
  Conf Proc IEEE Eng Med Biol Soc, 1, 3470-3473.  
16434398 U.Zachariae, T.Klühspies, S.De, H.Engelhardt, and K.Zeth (2006).
High resolution crystal structures and molecular dynamics studies reveal substrate binding in the porin Omp32.
  J Biol Chem, 281, 7413-7420.
PDB codes: 2fgq 2fgr
15647112 P.G.Bagos, T.D.Liakopoulos, and S.J.Hamodrakas (2005).
Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method.
  BMC Bioinformatics, 6, 7.  
16132085 S.Connelly, K.Line, M.N.Isupov, and J.A.Littlechild (2005).
Synthesis and characterisation of a ligand that forms a stable tetrahedral intermediate in the active site of the Aureobacterium species (-) gamma-lactamase.
  Org Biomol Chem, 3, 3260-3262.  
  15215418 F.S.Berven, K.Flikka, H.B.Jensen, and I.Eidhammer (2004).
BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria.
  Nucleic Acids Res, 32, W394-W399.  
14978719 M.M.Gromiha, S.Ahmad, and M.Suwa (2004).
Neural network-based prediction of transmembrane beta-strand segments in outer membrane proteins.
  J Comput Chem, 25, 762-767.  
15162482 N.K.Natt, H.Kaur, and G.P.Raghava (2004).
Prediction of transmembrane regions of beta-barrel proteins using ANN- and SVM-based methods.
  Proteins, 56, 11-18.  
14763978 S.Grizot, and S.K.Buchanan (2004).
Structure of the OmpA-like domain of RmpM from Neisseria meningitidis.
  Mol Microbiol, 51, 1027-1037.
PDB code: 1r1m
12501242 C.Heinz, H.Engelhardt, and M.Niederweis (2003).
The core of the tetrameric mycobacterial porin MspA is an extremely stable beta-sheet domain.
  J Biol Chem, 278, 8678-8685.  
14665678 H.Nikaido (2003).
Molecular basis of bacterial outer membrane permeability revisited.
  Microbiol Mol Biol Rev, 67, 593-656.  
12716881 L.Vandeputte-Rutten, M.P.Bos, J.Tommassen, and P.Gros (2003).
Crystal structure of Neisserial surface protein A (NspA), a conserved outer membrane protein with vaccine potential.
  J Biol Chem, 278, 24825-24830.
PDB code: 1p4t
12704154 S.Galdiero, D.Capasso, M.Vitiello, M.D'Isanto, C.Pedone, and M.Galdiero (2003).
Role of surface-exposed loops of Haemophilus influenzae protein P2 in the mitogen-activated protein kinase cascade.
  Infect Immun, 71, 2798-2809.  
12885642 U.Zachariae, V.Helms, and H.Engelhardt (2003).
Multistep mechanism of chloride translocation in a strongly anion-selective porin channel.
  Biophys J, 85, 954-962.  
11746705 A.Koumanov, H.Rüterjans, and A.Karshikoff (2002).
Continuum electrostatic analysis of irregular ionization and proton allocation in proteins.
  Proteins, 46, 85-96.  
11959503 B.Byrne, and S.Iwata (2002).
Membrane protein complexes.
  Curr Opin Struct Biol, 12, 239-243.  
12183233 M.Olesky, M.Hobbs, and R.A.Nicholas (2002).
Identification and analysis of amino acid mutations in porin IB that mediate intermediate-level resistance to penicillin and tetracycline in Neisseria gonorrhoeae.
  Antimicrob Agents Chemother, 46, 2811-2820.  
12021430 U.Zachariae, A.Koumanov, H.Engelhardt, and A.Karshikoff (2002).
Electrostatic properties of the anion selective porin Omp32 from Delftia acidovorans and of the arginine cluster of bacterial porins.
  Protein Sci, 11, 1309-1319.  
11589692 A.Sharff, C.Fanutti, J.Shi, C.Calladine, and B.Luisi (2001).
The role of the TolC family in protein transport and multidrug efflux. From stereochemical certainty to mechanistic hypothesis.
  Eur J Biochem, 268, 5011-5026.  
11274469 I.Jacoboni, P.L.Martelli, P.Fariselli, V.De Pinto, and R.Casadio (2001).
Prediction of the transmembrane regions of beta-barrel membrane proteins with a neural network-based predictor.
  Protein Sci, 10, 779-787.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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