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(-) Description

Title :  HINGE-BENDING MOTION OF D-ALLOSE BINDING PROTEIN FROM ESCHERICHIA COLI: THREE OPEN CONFORMATIONS
 
Authors :  U. Magnusson, B. N. Chaudhuri, J. Ko, C. Park, T. A. Jones, S. L. Mowbray
Date :  24 Jan 02  (Deposition) - 06 Mar 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Periplasmic Binding Protein, Allose, X-Ray Crystallography, Hinge Bending, Conformational Change (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. N. Chaudhuri, J. Ko, C. Park, T. A. Jones, S. L. Mowbray
Structure Of D-Allose Binding Protein From Escherichia Coli Bound To D-Allose At 1. 8 A Resolution
J. Mol. Biol. V. 286 1519 1999
PubMed-ID: 10064713  |  Reference-DOI: 10.1006/JMBI.1999.2571
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - D-ALLOSE-BINDING PERIPLASMIC PROTEIN
    Chains: A, B
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: ALBP

 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  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1ZN8Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:182 , HOH A:2252 , HOH A:2253 , HOH A:2254 , GLU B:277BINDING SITE FOR RESIDUE ZN A1289
2AC2SOFTWAREGLU A:157 , HOH A:2255 , GLU B:135BINDING SITE FOR RESIDUE ZN A1290
3AC3SOFTWAREGLU A:3 , ASP A:35 , ASP B:18BINDING SITE FOR RESIDUE ZN A1291
4AC4SOFTWAREGLU A:237 , GLU A:264 , GLN A:288 , HOH A:2256 , HOH A:2257BINDING SITE FOR RESIDUE ZN A1292
5AC5SOFTWARELYS A:120 , ASP A:282 , GLU B:264 , HOH B:2228 , HOH B:2229 , HOH B:2230BINDING SITE FOR RESIDUE ZN B1289
6AC6SOFTWAREALA B:1 , HOH B:2231 , HOH B:2232 , HOH B:2233 , HOH B:2234BINDING SITE FOR RESIDUE ZN B1290
7AC7SOFTWAREGLU A:132 , GLU B:132 , HOH B:2235 , HOH B:2236 , HOH B:2237BINDING SITE FOR RESIDUE ZN B1291
8AC8SOFTWAREGLU A:53 , GLN B:50 , GLU B:53 , HOH B:2238 , HOH B:2239 , HOH B:2240BINDING SITE FOR RESIDUE ZN B1292

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1GUD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1GUD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GUD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1GUD)

(-) Exons   (0, 0)

(no "Exon" information available for 1GUD)

(-) 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:288
 aligned with ALSB_ECOLI | P39265 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:288
                                    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        
           ALSB_ECOLI    24 AAEYAVVLKTLSNPFWVDMKKGIEDEAKTLGVSVDIFASPSEGDFQSQLQLFEDLSNKNYKGIAFAPLSSVNLVMPVARAWKKGIYLVNLDEKIDMDNLKKAGGNVEAFVTTDNVAVGAKGASFIIDKLGAEGGEVAIIEGKAGNASGEARRNGATEAFKKASQIKLVASQPADWDRIKALDVATNVLQRNPNIKAIYCANDTMAMGVAQAVANAGKTGKVLVVGTDGIPEARKMVEAGQMTATVAQNPADIGATGLKLMVDAEKSGKVIPLDKAPEFKLVDSILVTQ 311
               SCOP domains d1guda_ A: D-allose-binding protein                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1gudA01 A:1-110,A:250-278  [code=3.40.50.2300, no name defined]                                               1gudA02 A:111-249,A:279-288  [code=3.40.50.2300, no name defined]                                                                          1gudA01 A:1-110,A:250-278    1gudA02    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhh..eeeee....hhhhhhhh.....eeee.hhhhhhhhhhhhhhhhhhhhheeeeeee....hhhhhhhhhhhhhhhhh...eeeeeeee...hhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhh......eeeee..hhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhh..........eeee...eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1gud A   1 AAEYAVVLKTLSNPFWVDMKKGIEDEAKTLGVSVDIFASPSEGDFQSQLQLFEDLSNKNYKGIAFAPLSSVNLVMPVARAWKKGIYLVNLDEKIDMDNLKKAGGNVEAFVTTDNVAVGAKGASFIIDKLGAEGGEVAIIEGKAGNASGEARRNGATEAFKKASQIKLVASQPADWDRIKALDVATNVLQRNPNIKAIYCANDTMAMGVAQAVANAGKTGKVLVVGTDGIPEARKMVEAGQMTATVAQNPADIGATGLKLMVDAEKSGKVIPLDKAPEFKLVDSILVTQ 288
                                    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        


Chain B from PDB  Type:PROTEIN  Length:288
 aligned with ALSB_ECOLI | P39265 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:288
                                    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        
           ALSB_ECOLI    24 AAEYAVVLKTLSNPFWVDMKKGIEDEAKTLGVSVDIFASPSEGDFQSQLQLFEDLSNKNYKGIAFAPLSSVNLVMPVARAWKKGIYLVNLDEKIDMDNLKKAGGNVEAFVTTDNVAVGAKGASFIIDKLGAEGGEVAIIEGKAGNASGEARRNGATEAFKKASQIKLVASQPADWDRIKALDVATNVLQRNPNIKAIYCANDTMAMGVAQAVANAGKTGKVLVVGTDGIPEARKMVEAGQMTATVAQNPADIGATGLKLMVDAEKSGKVIPLDKAPEFKLVDSILVTQ 311
               SCOP domains d1gudb_ B: D-allose-binding protein                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1gudB01 B:1-110,B:250-278  [code=3.40.50.2300, no name defined]                                               1gudB02 B:111-249,B:279-288  [code=3.40.50.2300, no name defined]                                                                          1gudB01 B:1-110,B:250-278    1gudB02    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhhhhhh....eeee.......hhhhhhhhhhh..eeeee....hhhhhhhh.....eeee.hhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhhhh...eeeeeeee...hhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhh..........eeee...eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1gud B   1 AAEYAVVLKTLSNPFWVDMKKGIEDEAKTLGVSVDIFASPSEGDFQSQLQLFEDLSNKNYKGIAFAPLSSVNLVMPVARAWKKGIYLVNLDEKIDMDNLKKAGGNVEAFVTTDNVAVGAKGASFIIDKLGAEGGEVAIIEGKAGNASGEARRNGATEAFKKASQIKLVASQPADWDRIKALDVATNVLQRNPNIKAIYCANDTMAMGVAQAVANAGKTGKVLVVGTDGIPEARKMVEAGQMTATVAQNPADIGATGLKLMVDAEKSGKVIPLDKAPEFKLVDSILVTQ 288
                                    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
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GUD)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ALSB_ECOLI | P39265)
molecular function
    GO:0015145    monosaccharide transmembrane transporter activity    Enables the transfer of a monosaccharide from one side of a membrane to the other.
biological process
    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:0015749    monosaccharide transport    The directed movement of monosaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monosaccharides are the simplest carbohydrates; they are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
    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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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).
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ALSB_ECOLI | P39265: 1gub 1rpj

(-) Related Entries Specified in the PDB File

1gub HINGE-BENDING MOTION OF D-ALLOSE BINDING PROTEIN FROM ESCHERICHIA COLI: THREE OPEN CONFORMATIONS
1rpj CRYSTAL STRUCTURE OF D-ALLOSE BINDING PROTEIN FROMESCHERICHIA COLI