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(-) Description

Title :  CRYSTAL STRUCTURE OF SUGAR ABC TRANSPORTER, ATP-BINDING PROTEIN
 
Authors :  A. S. Ethayathullah, Y. Bessho, B. Padmanabhan, T. P. Singh, P. Kaur, S. Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  02 May 07  (Deposition) - 06 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.11
Chains :  Asym./Biol. Unit :  A
Keywords :  Sugar Transport, Atp Binding, Alpha And Beta Proteins (A/B) Class, Tm0421, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Ethayathullah, Y. Bessho, B. Padmanabhan, T. P. Singh, P. Kaur, S. Yokoyama
Crystal Structure Of Sugar Abc Transporter, Atp-Binding Protein
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUGAR ABC TRANSPORTER, ATP-BINDING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: MSB8

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:37 , GLY A:39 , CYS A:40 , GLY A:41 , LYS A:42 , THR A:43 , HOH A:2074BINDING SITE FOR RESIDUE SO4 A 1001
2AC2SOFTWARETYR A:12 , GLY A:14 , SER A:135 , GLN A:138 , ARG A:141 , HOH A:2042 , HOH A:2111 , HOH A:2246BINDING SITE FOR RESIDUE SO4 A 1002
3AC3SOFTWAREPHE A:13 , HIS A:89 , PHE A:98BINDING SITE FOR RESIDUE PEG A 2001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:236 -Pro A:237

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YYZ)

(-) Sequences/Alignments

Asymmetric/Biological 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:358
 aligned with Q9WYQ2_THEMA | Q9WYQ2 from UniProtKB/TrEMBL  Length:359

    Alignment length:358
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351        
         Q9WYQ2_THEMA     2 PSIRVVNLKKYFGKVKAVDGVSFEVKDGEFVALLGPSGCGKTTTLLMLAGIYKPTSGEIYFDDVLVNDIPPKYREVGMVFQNYALYPHMTVFENIAFPLRARRISKDEVEKRVVEIARKLLIDNLLDRKPTQLSGGQQQRVALARALVKQPKVLLFDEPLSNLDANLRMIMRAEIKHLQQELGITSVYVTHDQAEAMTMASRIAVFNQGKLVQYGTPDEVYDSPKNMFVASFIGNPPTNFLRDFSVSVENKQTILKRDDVIIKLPEPVDVKLKEVVVGIRPEHCRISRERVENSIPGVVYVVEPLGRDIIVNVKTEKGEIIKVFGDTGKAPQPGENVFLVPDLRKIHLFNPETEETIL 359
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------ABC_tran-2yyzA02 A:43-162                                                                                               -------------------------------------------------------------------------------------------------------------------TOBE_2-2yyzA01 A:278-350                                                 --------- Pfam domains
         Sec.struct. author ..eeeeeeeeee..eeeeeeeeeee....eeeee.....hhhhhhhhhh......eeeeee..ee....hhhhh.eeee..........hhhhhhhhhhh...hhhhh.hhhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhh.eeeeee..eeeeeehhhhhhhh..hhhhhhhh.....eeeeeeeeeee..eeeeee..eeee..........eeeeeehhh.eeee.......eeeeeeeeeee..eeeeeeee....eeeee...........eeeeee.....eee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yyz A   2 PSIRVVNLKKYFGKVKAVDGVSFEVKDGEFVALLGPSGCGKTTTLLMLAGIYKPTSGEIYFDDVLVNDIPPKYREVGMVFQNYALYPHMTVFENIAFPLRARRISKDEVEKRVVEIARKLLIDNLLDRKPTQLSGGQQQRVALARALVKQPKVLLFDEPLSNLDANLRMIMRAEIKHLQQELGITSVYVTHDQAEAMTMASRIAVFNQGKLVQYGTPDEVYDSPKNMFVASFIGNPPTNFLRDFSVSVENKQTILKRDDVIIKLPEPVDVKLKEVVVGIRPEHCRISRERVENSIPGVVYVVEPLGRDIIVNVKTEKGEIIKVFGDTGKAPQPGENVFLVPDLRKIHLFNPETEETIL 359
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351
   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 2YYZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YYZ)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: OB (224)
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9WYQ2_THEMA | Q9WYQ2)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0016820    hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances    Catalysis of the hydrolysis of an acid anhydride to directly drive the transport of a substance across a membrane.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    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:0043190    ATP-binding cassette (ABC) transporter complex    A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.

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