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(-) Description

Title :  STRUCTURE OF THE ZINC TRANSPORTER YIIP
 
Authors :  M. Lu
Date :  27 Jun 07  (Deposition) - 16 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Zinc Transporter, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Lu, D. Fu
Structure Of The Zinc Transporter Yiip.
Science V. 317 1746 2007
PubMed-ID: 17717154  |  Reference-DOI: 10.1126/SCIENCE.1143748

(-) Compounds

Molecule 1 - FERROUS-IRON EFFLUX PUMP FIEF
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL21/DE3
    Expression System Plasmid: PET15B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FIEF
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric Unit (1, 7)
No.NameCountTypeFull Name
1ZN7Ligand/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  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:232 , ILE B:245 , ASP B:285 , VAL B:289BINDING SITE FOR RESIDUE ZN B 301
2AC2SOFTWAREHIS A:261 , ASP A:265 , HIS A:283 , ASP A:285 , ZN A:306BINDING SITE FOR RESIDUE ZN A 302
3AC3SOFTWAREALA A:67 , ASP A:68 , SER A:72 , HIS A:75BINDING SITE FOR RESIDUE ZN A 303
4AC4SOFTWAREHIS B:261 , ASP B:265 , HIS B:283 , ASP B:285BINDING SITE FOR RESIDUE ZN B 304
5AC5SOFTWAREALA B:67 , ASP B:68 , SER B:72 , HIS B:75BINDING SITE FOR RESIDUE ZN B 305
6AC6SOFTWAREHIS A:232 , ILE A:245 , ASP A:285 , ZN A:302BINDING SITE FOR RESIDUE ZN A 306
7AC7SOFTWAREASP A:45 , ASP A:49 , ASP A:157BINDING SITE FOR RESIDUE ZN A 307

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:275 -Pro A:276
2Phe B:275 -Pro B:276

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2QFI)

(-) 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:286
 aligned with FIEF_ECOLI | P69380 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:286
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284      
           FIEF_ECOLI     5 YGRLVSRAAIAATAMASLLLLIKIFAWWYTGSVSILAALVDSLVDIGASLTNLLVVRYSLQPADDNHSFGHGKAESLAALAQSMFISGSALFLFLTGIQHLISPTPMTDPGVGVIVTIVALICTIILVSFQRWVVRRTQSQAVRADMLHYQSDVMMNGAILLALGLSWYGWHRADALFALGIGIYILYSALRMGYEAVQSLLDRALPDEERQEIIDIVTSWPGVSGAHDLRTRQSGPTRFIQIHLEMEDSLPLVQAHMVADQVEQAILRRFPGSDVIIHQDPCSVV 290
               SCOP domains d2qfia2 A:5-208 Ferrous-iron efflux pump FieF                                                                                                                                                               d2qfia1 A:209-290 Ferrous-iron efflux pump FieF (YiiP)                             SCOP domains
               CATH domains 2qfiA01 A:5-205 Cation efflux protein cytoplasmic domain-like                                                                                                                                            2qfiA02 A:206-290 Cation efflux protein cytoplasmic domain-like                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh...........................hhhhhhhhhhhhhhhh...............hhhhhhhhh.........hhhhh.....................hhhhh.hhhhhh.hhhhhhhhh....hhhhhhhhhhhh.......................hhhhhh........hhhhhhhhhh.......hhhhhhhhhhh.................................hhhhhhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qfi A   5 YGRLVSRAAIAATAMASLLLLIKIFAWWYTGSVSILAALVDSLVDIGASLTNLLVVRYSLQPADDNHSFGHGKAESLAALAQSMFISGSALFLFLTGIQHLISPTPMTDPGVGVIVTIVALICTIILVSFQRWVVRRTQSQAVRADMLHYQSDVMMNGAILLALGLSWYGWHRADALFALGIGIYILYSALRMGYEAVQSLLDRALPDEERQEIIDIVTSWPGVSGAHDLRTRQSGPTRFIQIHLEMEDSLPLVQAHMVADQVEQAILRRFPGSDVIIHQDPCSVV 290
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284      


Chain B from PDB  Type:PROTEIN  Length:286
 aligned with FIEF_ECOLI | P69380 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:286
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284      
           FIEF_ECOLI     5 YGRLVSRAAIAATAMASLLLLIKIFAWWYTGSVSILAALVDSLVDIGASLTNLLVVRYSLQPADDNHSFGHGKAESLAALAQSMFISGSALFLFLTGIQHLISPTPMTDPGVGVIVTIVALICTIILVSFQRWVVRRTQSQAVRADMLHYQSDVMMNGAILLALGLSWYGWHRADALFALGIGIYILYSALRMGYEAVQSLLDRALPDEERQEIIDIVTSWPGVSGAHDLRTRQSGPTRFIQIHLEMEDSLPLVQAHMVADQVEQAILRRFPGSDVIIHQDPCSVV 290
               SCOP domains d2qfib2 B:5-208 Ferrous-iron efflux pump FieF                                                                                                                                                               d2qfib1 B:209-290 Ferrous-iron efflux pump FieF (YiiP)                             SCOP domains
               CATH domains 2qfiB01 B:5-205 Cation efflux protein cytoplasmic domain-like                                                                                                                                            2qfiB02 B:206-290 Cation efflux protein cytoplasmic domain-like                       CATH domains
           Pfam domains (1) --------Cation_efflux-2qfiB01 B:13-290                                                                                                                                                                                                                                                         Pfam domains (1)
           Pfam domains (2) --------Cation_efflux-2qfiB02 B:13-290                                                                                                                                                                                                                                                         Pfam domains (2)
         Sec.struct. author ........hhhhhh...........................hhhhhhhhhhhhhhhh...............hhhhhhhhh.........hhhhh.....................hhhhh.hhhhhh.hhhhhhhhh....hhhhhhhhhhhh.......................hhhhhhhhh.....hhhhhhhhhh.......hhhhhhhhhhh.................................hhhhhhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qfi B   5 YGRLVSRAAIAATAMASLLLLIKIFAWWYTGSVSILAALVDSLVDIGASLTNLLVVRYSLQPADDNHSFGHGKAESLAALAQSMFISGSALFLFLTGIQHLISPTPMTDPGVGVIVTIVALICTIILVSFQRWVVRRTQSQAVRADMLHYQSDVMMNGAILLALGLSWYGWHRADALFALGIGIYILYSALRMGYEAVQSLLDRALPDEERQEIIDIVTSWPGVSGAHDLRTRQSGPTRFIQIHLEMEDSLPLVQAHMVADQVEQAILRRFPGSDVIIHQDPCSVV 290
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284
   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  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: DMT (2)

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (FIEF_ECOLI | P69380)
molecular function
    GO:0015086    cadmium ion transmembrane transporter activity    Enables the transfer of cadmium (Cd) ions from one side of a membrane to the other.
    GO:0008324    cation transmembrane transporter activity    Enables the transfer of cation from one side of the membrane to the other.
    GO:0015093    ferrous iron transmembrane transporter activity    Enables the transfer of ferrous iron (Fe(II) or Fe2+) ions from one side of a membrane to the other.
    GO:0046873    metal ion transmembrane transporter activity    Enables the transfer of metal ions from one side of a membrane to the other.
    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.
    GO:0015341    zinc efflux active transmembrane transporter activity    Catalysis of the transfer of a zinc ion or zinc ions from the inside of the cell to the outside of the cell across a membrane: Zn2+(out) = Zn2+(in). The activity is driven by proton motive force.
biological process
    GO:0070574    cadmium ion transmembrane transport    A process in which a cadmium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0015691    cadmium ion transport    The directed movement of cadmium (Cd) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0098655    cation transmembrane transport    A process in which a cation is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006812    cation transport    The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006876    cellular cadmium ion homeostasis    Any process involved in the maintenance of an internal steady state of cadmium ions at the level of a cell.
    GO:0006882    cellular zinc ion homeostasis    Any process involved in the maintenance of an internal steady state of zinc ions at the level of a cell.
    GO:1903874    ferrous iron transmembrane transport    The directed movement of ferrous iron (iron(2+)) across a membrane.
    GO:0015684    ferrous iron transport    The directed movement of ferrous iron (Fe(II) or Fe2+) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0055072    iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell.
    GO:0061088    regulation of sequestering of zinc ion    Any process that modulates the rate, frequency, or extent of sequestering of zinc ion. Sequestering of zinc ion is the process of binding or confining zinc ions such that they are separated from other components of a biological system.
    GO:0010043    response to zinc ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a zinc ion stimulus.
    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.
    GO:0071577    zinc II ion transmembrane transport    A process in which a zinc II ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006829    zinc II ion transport    The directed movement of zinc (Zn II) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
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: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

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        FIEF_ECOLI | P69380: 3h90

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