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PDBsum entry 1a0t
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Outer membrane protein PDB id
1a0t

 

 

 

 

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Contents
Protein chains
413 a.a. *
Ligands
GLC-FRU ×6
Metals
_CA ×3
Waters ×330
* Residue conservation analysis
PDB id:
1a0t
Name: Outer membrane protein
Title: Sucrose-specific porin, with bound sucrose molecules
Structure: Sucrose-specific porin. Chain: p, q, r. Engineered: yes
Source: Salmonella typhimurium. Organism_taxid: 602. Cellular_location: outer membrane. Gene: scry. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: ks 26.
Biol. unit: Trimer (from PDB file)
Resolution:
2.40Å     R-factor:   0.207     R-free:   0.246
Authors: K.Diederichs,W.Welte
Key ref: D.Forst et al. (1998). Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose. Nat Struct Biol, 5, 37-46. PubMed id: 9437428
Date:
08-Dec-97     Release date:   18-Mar-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
P22340  (SCRY_SALTM) -  Sucrose porin from Salmonella typhimurium
Seq:
Struc: 		505 a.a.
413 a.a.
Key:    Secondary structure  CATH domain

 

 
Nat Struct Biol 5:37-46 (1998)
PubMed id: 9437428  
 
 
Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose.
D.Forst, W.Welte, T.Wacker, K.Diederichs.
 
  ABSTRACT  
 
The X-ray structure of a sucrose-specific porin (ScrY) from Salmonella typhimurium has been determined by multiple isomorphous replacement at 2.4 A resolution both in its uncomplexed form and with bound sucrose. ScrY is a noncrystallographic trimer of identical subunits, each with 413 structurally well-defined amino acids. A monomer is built up of 18 anti-parallel beta-strands surrounding a hydrophilic pore, with a topology closely similar to that of maltoporin. Two non-overlapping sucrose-binding sites were identified in difference Fourier maps. The higher permeability for sucrose of ScrY as compared to maltoporin is mainly accounted for by differences in their pore-lining residues.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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Structural basis for solute transport, nucleotide regulation, and immunological recognition of Neisseria meningitidis PorB.
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PDB codes: 3a2r 3a2s 3a2t 3a2u 3vzt 3vzu 3vzw
19421989 Y.Y.Ou, S.A.Chen, and M.M.Gromiha (2010).
Prediction of membrane spanning segments and topology in beta-barrel membrane proteins at better accuracy.
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Finding and characterizing tunnels in macromolecules with application to ion channels and pores.
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Evidence for the transport of maltose by the sucrose permease, CscB, of Escherichia coli.
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18800046 C.Tatko (2008).
Sugars stack up.
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18625734 G.R.Nielubowicz, S.N.Smith, and H.L.Mobley (2008).
Outer membrane antigens of the uropathogen Proteus mirabilis recognized by the humoral response during experimental murine urinary tract infection.
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18611376 S.Biswas, M.M.Mohammad, L.Movileanu, and B.van den Berg (2008).
Crystal structure of the outer membrane protein OpdK from Pseudomonas aeruginosa.
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PDB code: 2qtk
17505114 J.G.Wittmann, and M.G.Rudolph (2007).
Pseudo-merohedral twinning in monoclinic crystals of human orotidine-5'-monophosphate decarboxylase.
  Acta Crystallogr D Biol Crystallogr, 63, 744-749.  
17557843 N.de María, A.Guevara, M.T.Serra, I.García-Luque, A.González-Sama, M.García de Lacoba, M.R.de Felipe, and M.Fernández-Pascual (2007).
Putative porin of Bradyrhizobium sp. (Lupinus) bacteroids induced by glyphosate.
  Appl Environ Microbiol, 73, 5075-5082.  
16424900 I.Iacovache, P.Paumard, H.Scheib, C.Lesieur, N.Sakai, S.Matile, M.W.Parker, and F.G.van der Goot (2006).
A rivet model for channel formation by aerolysin-like pore-forming toxins.
  EMBO J, 25, 457-466.  
16888630 O.Yildiz, K.R.Vinothkumar, P.Goswami, and W.Kühlbrandt (2006).
Structure of the monomeric outer-membrane porin OmpG in the open and closed conformation.
  EMBO J, 25, 3702-3713.
PDB codes: 2iwv 2iww
16790931 R.C.Hillig, and L.Renault (2006).
Detecting and overcoming hemihedral twinning during the MIR structure determination of Rna1p.
  Acta Crystallogr D Biol Crystallogr, 62, 750-765.
PDB code: 2ca6
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
15739205 D.P.Chimento, R.J.Kadner, and M.C.Wiener (2005).
Comparative structural analysis of TonB-dependent outer membrane transporters: implications for the transport cycle.
  Proteins, 59, 240-251.  
16204348 K.J.Park, M.M.Gromiha, P.Horton, and M.Suwa (2005).
Discrimination of outer membrane proteins using support vector machines.
  Bioinformatics, 21, 4223-4229.  
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.  
  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.  
15141026 H.R.Bigelow, D.S.Petrey, J.Liu, D.Przybylski, and B.Rost (2004).
Predicting transmembrane beta-barrels in proteomes.
  Nucleic Acids Res, 32, 2566-2577.  
15601207 I.Kosztin, and K.Schulten (2004).
Fluctuation-driven molecular transport through an asymmetric membrane channel.
  Phys Rev Lett, 93, 238102.  
15272310 J.Ye, and B.van den Berg (2004).
Crystal structure of the bacterial nucleoside transporter Tsx.
  EMBO J, 23, 3187-3195.
PDB codes: 1tlw 1tly 1tlz
15315948 M.Baaden, and M.S.Sansom (2004).
OmpT: molecular dynamics simulations of an outer membrane enzyme.
  Biophys J, 87, 2942-2953.  
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.  
14581200 D.Lu, P.Grayson, and K.Schulten (2003).
Glycerol conductance and physical asymmetry of the Escherichia coli glycerol facilitator GlpF.
  Biophys J, 85, 2977-2987.  
14665678 H.Nikaido (2003).
Molecular basis of bacterial outer membrane permeability revisited.
  Microbiol Mol Biol Rev, 67, 593-656.  
12925992 Q.Vicens, and E.Westhof (2003).
Molecular recognition of aminoglycoside antibiotics by ribosomal RNA and resistance enzymes: an analysis of x-ray crystal structures.
  Biopolymers, 70, 42-57.  
12446642 A.R.Duguay, and T.J.Silhavy (2002).
Signal sequence mutations as tools for the characterization of LamB folding intermediates.
  J Bacteriol, 184, 6918-6928.  
12185084 C.Andersen, B.Schiffler, A.Charbit, and R.Benz (2002).
PH-induced collapse of the extracellular loops closes Escherichia coli maltoporin and allows the study of asymmetric sugar binding.
  J Biol Chem, 277, 41318-41325.  
11964234 F.Orlik, C.Andersen, and R.Benz (2002).
Site-directed mutagenesis of tyrosine 118 within the central constriction site of the LamB (Maltoporin) channel of Escherichia coli. I. Effect on ion transport.
  Biophys J, 82, 2466-2475.  
12080122 F.Orlik, C.Andersen, and R.Benz (2002).
Site-directed mutagenesis of tyrosine 118 within the central constriction site of the LamB (maltoporin) channel of Escherichia coli. II. Effect on maltose and maltooligosaccharide binding kinetics.
  Biophys J, 83, 309-321.  
12021455 J.Michels, A.Geyer, V.Mocanu, W.Welte, A.L.Burlingame, and M.Przybylski (2002).
Structure and functional characterization of the periplasmic N-terminal polypeptide domain of the sugar-specific ion channel protein (ScrY porin).
  Protein Sci, 11, 1565-1574.  
12003940 P.Van Gelder, F.Dumas, I.Bartoldus, N.Saint, A.Prilipov, M.Winterhalter, Y.Wang, A.Philippsen, J.P.Rosenbusch, and T.Schirmer (2002).
Sugar transport through maltoporin of Escherichia coli: role of the greasy slide.
  J Bacteriol, 184, 2994-2999.  
12220498 R.Dutzler, T.Schirmer, M.Karplus, and S.Fischer (2002).
Translocation mechanism of long sugar chains across the maltoporin membrane channel.
  Structure, 10, 1273-1284.  
11790840 W.C.Wimley (2002).
Toward genomic identification of beta-barrel membrane proteins: composition and architecture of known structures.
  Protein Sci, 11, 301-312.  
12192075 Y.Zhai, and M.H.Saier (2002).
The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes.
  Protein Sci, 11, 2196-2207.  
11571189 D.Parke, M.A.Garcia, and L.N.Ornston (2001).
Cloning and genetic characterization of dca genes required for beta-oxidation of straight-chain dicarboxylic acids in Acinetobacter sp. strain ADP1.
  Appl Environ Microbiol, 67, 4817-4827.  
11133980 E.Maier, G.Polleichtner, B.Boeck, R.Schinzel, and R.Benz (2001).
Identification of the outer membrane porin of Thermus thermophilus HB8: the channel-forming complex has an unusually high molecular mass and an extremely large single-channel conductance.
  J Bacteriol, 183, 800-803.  
11406106 F.S.Cordes, A.Kukol, L.R.Forrest, I.T.Arkin, M.S.Sansom, and W.B.Fischer (2001).
The structure of the HIV-1 Vpu ion channel: modelling and simulation studies.
  Biochim Biophys Acta, 1512, 291-298.  
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.  
11371453 T.Páli, and D.Marsh (2001).
Tilt, twist, and coiling in beta-barrel membrane proteins: relation to infrared dichroism.
  Biophys J, 80, 2789-2797.  
10848998 C.Jansen, M.Heutink, J.Tommassen, and H.de Cock (2000).
The assembly pathway of outer membrane protein PhoE of Escherichia coli.
  Eur J Biochem, 267, 3792-3800.  
10981633 G.E.Schulz (2000).
beta-Barrel membrane proteins.
  Curr Opin Struct Biol, 10, 443-447.  
10966478 J.L.Popot, and D.M.Engelman (2000).
Helical membrane protein folding, stability, and evolution.
  Annu Rev Biochem, 69, 881-922.  
10986465 K.Zeth, K.Diederichs, W.Welte, and H.Engelhardt (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.
PDB code: 1e54
10821691 M.Sahin-Tóth, and H.R.Kaback (2000).
Functional conservation in the putative substrate binding site of the sucrose permease from Escherichia coli.
  Biochemistry, 39, 6170-6175.  
10819976 M.Sahin-Tóth, K.M.Akhoon, J.Runner, and H.R.Kaback (2000).
Ligand recognition by the lactose permease of Escherichia coli: specificity and affinity are defined by distinct structural elements of galactopyranosides.
  Biochemistry, 39, 5097-5103.  
10991194 S.M.Bezrukov, and M.Winterhalter (2000).
Examining noise sources at the single-molecule level: 1/f noise of an open maltoporin channel.
  Phys Rev Lett, 85, 202-205.  
10660614 T.Kasahara, and M.Kasahara (2000).
Three aromatic amino acid residues critical for galactose transport in yeast Gal2 transporter.
  J Biol Chem, 275, 4422-4428.  
10961503 Van Gelder P, F.Dumas, and M.Winterhalter (2000).
Understanding the function of bacterial outer membrane channels by reconstitution into black lipid membranes
  Biophys Chem, 85, 153-167.  
  10074088 C.Ulmke, J.Kreth, J.W.Lengeler, W.Welte, and K.Schmid (1999).
Site-directed mutagenesis of loop L3 of sucrose porin ScrY leads to changes in substrate selectivity.
  J Bacteriol, 181, 1920-1923.  
10611277 K.E.McAuley, P.K.Fyfe, J.P.Ridge, N.W.Isaacs, R.J.Cogdell, and M.R.Jones (1999).
Structural details of an interaction between cardiolipin and an integral membrane protein.
  Proc Natl Acad Sci U S A, 96, 14706-14711.
PDB code: 1qov
10209114 M.S.Sansom (1999).
Membrane proteins: A tale of barrels and corks.
  Curr Biol, 9, R254-R257.  
10449368 S.K.Buchanan (1999).
Beta-barrel proteins from bacterial outer membranes: structure, function and refolding.
  Curr Opin Struct Biol, 9, 455-461.  
9856937 A.D.Ferguson, E.Hofmann, J.W.Coulton, K.Diederichs, and W.Welte (1998).
Siderophore-mediated iron transport: crystal structure of FhuA with bound lipopolysaccharide.
  Science, 282, 2215-2220.
PDB codes: 1fcp 2fcp
  9684898 A.D.Ferguson, J.Breed, K.Diederichs, W.Welte, and J.W.Coulton (1998).
An internal affinity-tag for purification and crystallization of the siderophore receptor FhuA, integral outer membrane protein from Escherichia coli K-12.
  Protein Sci, 7, 1636-1638.  
9437417 B.K.Jap, and P.J.Walian (1998).
Gliding through sugar channels: how sweet it is!
  Nat Struct Biol, 5, 6-8.  
9786918 M.Kasahara, and M.Maeda (1998).
Contribution to substrate recognition of two aromatic amino acid residues in putative transmembrane segment 10 of the yeast sugar transporters Gal2 and Hxt2.
  J Biol Chem, 273, 29106-29112.  
9751640 R.M.Garavito (1998).
Membrane protein structures: the known world expands.
  Curr Opin Biotechnol, 9, 344-349.  
9786919 T.Kasahara, and M.Kasahara (1998).
Tryptophan 388 in putative transmembrane segment 10 of the rat glucose transporter Glut1 is essential for glucose transport.
  J Biol Chem, 273, 29113-29117.  
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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