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User:Cboursnell/Sandbox/Peripla BP 2

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Peripla_BP_2
periplasmic ferric siderophore binding protein fhud complexed with gallichrome
Identifiers
SymbolPeripla_BP_2
PfamPeripla_BP_2
InterProIPR002491
SCOP21efd / SCOPe / SUPFAM
TCDB3.A.1
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary

ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain.[1] The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site.[2][3][4] The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis.[5][6][7][8][9][10] The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions.[1] Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette.[1][11] More than 50 subfamilies have been described based on a phylogenetic and functional classification,,[1][2] [11]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). Most bacterial importers employ a periplasmic substrate-binding protein (PBP) that delivers the ligand to the extracellular gate of the TM domains. These proteins bind their substrates selectively and with high affinity, which is thought to ensure the specificity of the transport reaction. Binding proteins in Gram-negative bacteria are present within the periplasm, whereas those in Gram-positive bacteria are tethered tothe cell membrane via the acylation of a cysteine residue that is an integralcomponent of a lipoprotein signal sequence. In planta expression of a high-affinity iron-uptake system involving the siderophore chrysobactin in Erwinia chrysanthemi 3937 contributes greatly to invasive growth of this pathogen on its natural host, African violets.[12] The cobalamin (vitamin B12) andthe iron transport systems share many common attributes and probably evolvedfrom the same origin.[13][14] This entry represents of the periplasmic-binding domain is composed of two subdomains,each consisting of a central beta-sheet and surrounding alpha-helices, linkedby a rigid alpha-helix. The substrate binding site is locatedin a cleft between the two alpha/beta subdomains.[15] Category:Protein domains


References

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  1. ^ a b c d Saurin W, Hofnung M, Dassa E (January 1999). "Getting in or out: early segregation between importers and exporters in the evolution of ATP-binding cassette (ABC) transporters". J. Mol. Evol. 48 (1): 22–41. doi:10.1007/pl00006442. PMID 9873074.{{cite journal}}: CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)
  2. ^ a b Higgins CF (2001). "ABC transporters: physiology, structure and mechanism--an overview". Res. Microbiol. 152 (3–4): 205–10. doi:10.1016/s0923-2508(01)01193-7. PMID 11421269.
  3. ^ Higgins CF (1992). "ABC transporters: from microorganisms to man". Annu. Rev. Cell Biol. 8: 67–113. doi:10.1146/annurev.cb.08.110192.000435. PMID 1282354.
  4. ^ Schneider E, Hunke S (April 1998). "ATP-binding-cassette (ABC) transport systems: functional and structural aspects of the ATP-hydrolyzing subunits/domains". FEMS Microbiol. Rev. 22 (1): 1–20. doi:10.1111/j.1574-6976.1998.tb00358.x. PMID 9640644.{{cite journal}}: CS1 maint: date and year (link)
  5. ^ Kerr ID (March 2002). "Structure and association of ATP-binding cassette transporter nucleotide-binding domains". Biochim. Biophys. Acta. 1561 (1): 47–64. doi:10.1016/s0304-4157(01)00008-9. PMID 11988180.{{cite journal}}: CS1 maint: date and year (link)
  6. ^ Karpowich N, Martsinkevich O, Millen L, Yuan YR, Dai PL, MacVey K, Thomas PJ, Hunt JF (July 2001). "Crystal structures of the MJ1267 ATP binding cassette reveal an induced-fit effect at the ATPase active site of an ABC transporter". Structure. 9 (7): 571–86. doi:10.1016/s0969-2126(01)00617-7. PMID 11470432.{{cite journal}}: CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)
  7. ^ Yuan YR, Blecker S, Martsinkevich O, Millen L, Thomas PJ, Hunt JF (August 2001). "The crystal structure of the MJ0796 ATP-binding cassette. Implications for the structural consequences of ATP hydrolysis in the active site of an ABC transporter". J. Biol. Chem. 276 (34): 32313–21. doi:10.1074/jbc.M100758200. PMID 11402022.{{cite journal}}: CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)
  8. ^ Hung LW, Wang IX, Nikaido K, Liu PQ, Ames GF, Kim SH (December 1998). "Crystal structure of the ATP-binding subunit of an ABC transporter". Nature. 396 (6712): 703–7. doi:10.1038/25393. PMID 9872322.{{cite journal}}: CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)
  9. ^ Diederichs K, Diez J, Greller G, Müller C, Breed J, Schnell C, Vonrhein C, Boos W, Welte W (November 2000). "Crystal structure of MalK, the ATPase subunit of the trehalose/maltose ABC transporter of the archaeon Thermococcus litoralis". EMBO J. 19 (22): 5951–61. doi:10.1093/emboj/19.22.5951. PMC 305842. PMID 11080142.{{cite journal}}: CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)
  10. ^ Gaudet R, Wiley DC (September 2001). "Structure of the ABC ATPase domain of human TAP1, the transporter associated with antigen processing". EMBO J. 20 (17): 4964–72. doi:10.1093/emboj/20.17.4964. PMC 125601. PMID 11532960.{{cite journal}}: CS1 maint: date and year (link)
  11. ^ a b Dassa E, Bouige P (2001). "The ABC of ABCS: a phylogenetic and functional classification of ABC systems in living organisms". Res. Microbiol. 152 (3–4): 211–29. doi:10.1016/s0923-2508(01)01194-9. PMID 11421270.
  12. ^ Mahé B, Masclaux C, Rauscher L, Enard C, Expert D (October 1995). "Differential expression of two siderophore-dependent iron-acquisition pathways in Erwinia chrysanthemi 3937: characterization of a novel ferrisiderophore permease of the ABC transporter family". Mol. Microbiol. 18 (1): 33–43. doi:10.1111/j.1365-2958.1995.mmi_18010033.x. PMID 8596459.{{cite journal}}: CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)
  13. ^ Borths EL, Locher KP, Lee AT, Rees DC (December 2002). "The structure of Escherichia coli BtuF and binding to its cognate ATP binding cassette transporter". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16642–7. doi:10.1073/pnas.262659699. PMC 139197. PMID 12475936.{{cite journal}}: CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)
  14. ^ Sebulsky MT, Speziali CD, Shilton BH, Edgell DR, Heinrichs DE (December 2004). "FhuD1, a ferric hydroxamate-binding lipoprotein in Staphylococcus aureus: a case of gene duplication and lateral transfer". J. Biol. Chem. 279 (51): 53152–9. doi:10.1074/jbc.M409793200. PMID 15475351.{{cite journal}}: CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)
  15. ^ Karpowich NK, Huang HH, Smith PC, Hunt JF (March 2003). "Crystal structures of the BtuF periplasmic-binding protein for vitamin B12 suggest a functionally important reduction in protein mobility upon ligand binding". J. Biol. Chem. 278 (10): 8429–34. doi:10.1074/jbc.M212239200. PMID 12468528.{{cite journal}}: CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)
This article incorporates text from the public domain Pfam and InterPro: IPR002491
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