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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ARABINOSE BINDING PROTEIN WITH DESIGNED SEROTONIN BINDING SITE IN OPEN, LIGAND-FREE STATE
 
Authors :  B. Schreier, C. Stumpp, S. Wiesner, B. Hocker
Date :  03 Sep 09  (Deposition) - 13 Oct 09  (Release) - 17 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Sugar Transport, Arabinose Binding Protein, Periplasmic Binding Protein, Abp, Transport Protein, Periplasm, Receptor Design (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Schreier, C. Stumpp, S. Wiesner, B. Hocker
The Computational Design Of Ligand Binding Is Not A Solved Problem
Proc. Natl. Acad. Sci. Usa V. 106 18491 2009
PubMed-ID: 19833875  |  Reference-DOI: 10.1073/PNAS.0907950106

(-) Compounds

Molecule 1 - L-ARABINOSE-BINDING PERIPLASMIC PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: ABP, ARABINOSE BINDING PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2WRZ)

(-) Sites  (0, 0)

(no "Site" information available for 2WRZ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WRZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WRZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WRZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WRZ)

(-) Exons   (0, 0)

(no "Exon" information available for 2WRZ)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:300
 aligned with ARAF_ECOLI | P02924 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:300
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323
           ARAF_ECOLI    24 ENLKLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAVPDGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIVAKARGYDMKVIAVDDQFVNAKGKPMDTVPLVMMAATKIGERQGQELYKEMQKRGWDVKESAVMAITANELDTARRRTTGSMDALKAAGFPEKQIYQVPTKSNDIPGAFDAANSMLVQHPEVKHWLIVGMNDSTVLGGVRATEGQGFKAADIIGIGINGVDAVSELSKAQATGFYGSLLPSPDVHGYKSSEMLYNWVAKDVEPPKFTEVTDVVLITRDNFKEELEK 323
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2wrzA01 A:1-108,A:255-285  [code=3.40.50.2300, no name defined]                                             2wrzA02 A:109-254,A:286-300  [code=3.40.50.2300, no name defined]                                                                                 2wrzA01 A:1-108,A:255-285      2wrzA02         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee....hhhhhhhhhhhhhh......eeeeee....hhhhhhhhhhhhh.....eee.......hhhhhhhh......eee................eee...........hhhhhhhhhh..hhh.eeeeeee...hhhhhhhhh.hhhhhhhh..hhh.eeeee........hhhhhhhhhhh.....eeeee..hhhhhh...........hhh.ee.......hhhhhhh..........eee......hhhhhhhhhhhhhh.....eee...eee....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wrz A   1 ENLKLGFLVAQPEEPASQTQWKFADKAGKDLGFEVIKIAVPDGEKTLNAIDSLAASGAKGFVISTPDPKLGSAIVAKARGYDMKVIAVDNQFVNAKGKPMDTVPLVMEAATKIGERQGQELYKEMQKRGWDVKESAVMAITANELDTARRRTTGSMDALKAAGFPEKQIYQVPTKSEDIPGAFDAANSMLVQHPEVKHWLIVGMNDSTVLGGVRATEGQGFKAADIIGIGINGVDAVSELSKAQATGFYGSLLPSPDVHGYKSSEMLYNWVAKDVEPPKFTEVTDVVLITRDNFKEECEK 300
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300


Chain B from PDB  Type:PROTEIN  Length:295
 aligned with ARAF_ECOLI | P02924 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:295
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313     
           ARAF_ECOLI    24 ENLKLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAVPDGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIVAKARGYDMKVIAVDDQFVNAKGKPMDTVPLVMMAATKIGERQGQELYKEMQKRGWDVKESAVMAITANELDTARRRTTGSMDALKAAGFPEKQIYQVPTKSNDIPGAFDAANSMLVQHPEVKHWLIVGMNDSTVLGGVRATEGQGFKAADIIGIGINGVDAVSELSKAQATGFYGSLLPSPDVHGYKSSEMLYNWVAKDVEPPKFTEVTDVVLITRDNFK 318
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2wrzB01 B:1-109,B:257-283  [code=3.40.50.2300, no name defined]                                              2wrzB02 B:110-256,B:284-294  [code=3.40.50.2300, no name defined]                                                                                  2wrzB01 B:1-109,B:257-283  2wrzB02    - CATH domains
           Pfam domains (1) -Peripla_BP_1-2wrzB01 B:2-295                                                                                                                                                                                                                                                                           Pfam domains (1)
           Pfam domains (2) -Peripla_BP_1-2wrzB02 B:2-295                                                                                                                                                                                                                                                                           Pfam domains (2)
         Sec.struct. author ...eeeeee....hhhhhhhhhhhhhh......eeeeee....hhhhhhhhhhhhh.....eee.......hhhhhhhh......eee................eeee..........hhhhhhhhhh..hhh.eeeeeee...hhhhhhhhh.hhhhhhhh......eeeee........hhhhhhhhhhhh....eeeee..hhhhhh...........hhh.ee.......hhhhhhh..........eee......hhhhhhhhhhhhhh.....eeee..eee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wrz B   1 ENLKLGFLVAQPEEPASQTQWKFADKAGKDLGFEVIKIAVPDGEKTLNAIDSLAASGAKGFVISTPDPKLGSAIVAKARGYDMKVIAVDNQFVNAKGKPMDTVPLVMEAATKIGERQGQELYKEMQKRGWDVKESAVMAITANELDTARRRTTGSMDALKAAGFPEKQIYQVPTKSEDIPGAFDAANSMLVQHPEVKHWLIVGMNDSTVLGGVRATEGQGFKAADIIGIGINGVDAVSELSKAQATGFYGSLLPSPDVHGYKSSEMLYNWVAKDVEPPKFTEVTDVVLITRDNFK 295
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2WRZ)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Periplas_BP (97)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ARAF_ECOLI | P02924)
molecular function
    GO:0048029    monosaccharide binding    Interacting selectively and non-covalently with any monosaccharide. Monosaccharides are the simplest carbohydrates; they are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H[CHOH]nC(=O)[CHOH]mH with three or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
    GO:0015407    monosaccharide-transporting ATPase activity    Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + monosaccharide(out) = ADP + phosphate + monosaccharide(in). Ribose, xylose, arabinose, galactose and methylgalactoside are imported.
biological process
    GO:0042882    L-arabinose transport    The directed movement of L-arabinose, the L-enantiomer of arabinose, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0008643    carbohydrate transport    The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are any of a group of organic compounds based of the general formula Cx(H2O)y.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ARAF_ECOLI | P02924: 1abe 1abf 1apb 1bap 5abp 6abp 7abp 8abp 9abp

(-) Related Entries Specified in the PDB File

1abe 1abf 1apb 1bap 5abp 6abp 7abp 8abp 9abp