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(-) Description

Title :  STRUCTURAL BASIS FOR THE AUTOREGULATION OF THE ZINC TRANSPORTER YIIP
 
Authors :  M. Lu
Date :  29 Apr 09  (Deposition) - 08 Sep 09  (Release) - 20 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Membrane Protein, Zinc Transporter, Cell Inner Membrane, Cell Membrane, Ion Transport, Iron, Iron Transport, Membrane, Transmembrane, Transport, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Lu, J. Chai, D. Fu
Structural Basis For Autoregulation Of The Zinc Transporter Yiip.
Nat. Struct. Mol. Biol. V. 16 1063 2009
PubMed-ID: 19749753  |  Reference-DOI: 10.1038/NSMB.1662
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FERROUS-IRON EFFLUX PUMP FIEF
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 8-290
    GeneFIEF, YIIP, B3915, JW3886
    Organism ScientificESCHERICHIA COLI K-12
    Organism Taxid83333

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 24)

Asymmetric Unit (2, 24)
No.NameCountTypeFull Name
1HG8Ligand/IonMERCURY (II) ION
2ZN16Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1HG-1Ligand/IonMERCURY (II) ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1HG-1Ligand/IonMERCURY (II) ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:26 , CYS A:127BINDING SITE FOR RESIDUE HG A 2
02AC2SOFTWARECYS B:127BINDING SITE FOR RESIDUE HG B 4
03AC3SOFTWARESER C:229 , HOH C:340BINDING SITE FOR RESIDUE HG C 5
04AC4SOFTWARECYS C:127BINDING SITE FOR RESIDUE HG C 6
05AC5SOFTWARESER D:229BINDING SITE FOR RESIDUE HG D 7
06AC6SOFTWARECYS D:127BINDING SITE FOR RESIDUE HG D 291
07AC7SOFTWAREHIS A:261 , HIS C:283 , ASP C:285 , HOH C:294BINDING SITE FOR RESIDUE ZN C 1
08AC8SOFTWAREASP C:68 , HIS C:71 , HIS C:75 , HOH C:293BINDING SITE FOR RESIDUE ZN C 2
09AC9SOFTWAREHIS C:232 , HIS C:248 , ASP C:285 , HOH C:294 , HOH C:346BINDING SITE FOR RESIDUE ZN C 3
10BC1SOFTWAREASP A:45 , ASP A:49 , HIS A:153 , ASP A:157BINDING SITE FOR RESIDUE ZN A 4
11BC2SOFTWAREHIS B:261 , HOH B:307 , HIS D:283 , ASP D:285 , ZN D:292 , HOH D:335BINDING SITE FOR RESIDUE ZN D 5
12BC3SOFTWAREASP D:68 , HIS D:71 , HIS D:75 , HOH D:295BINDING SITE FOR RESIDUE ZN D 6
13BC4SOFTWAREZN D:5 , HIS D:232 , HIS D:248 , ASP D:285 , HOH D:294 , HOH D:335BINDING SITE FOR RESIDUE ZN D 292
14BC5SOFTWAREASP B:45 , ASP B:49 , HIS B:153 , ASP B:157BINDING SITE FOR RESIDUE ZN B 291
15BC6SOFTWAREHIS A:283 , ASP A:285 , HOH A:298 , HIS C:261BINDING SITE FOR RESIDUE ZN A 291
16BC7SOFTWAREASP A:68 , HIS A:71 , HIS A:75 , HOH A:295BINDING SITE FOR RESIDUE ZN A 292
17BC8SOFTWAREHIS A:232 , HIS A:248 , ASP A:285 , HOH A:294 , HOH A:298BINDING SITE FOR RESIDUE ZN A 293
18BC9SOFTWAREASP C:45 , ASP C:49 , HIS C:153 , ASP C:157BINDING SITE FOR RESIDUE ZN C 291
19CC1SOFTWAREHIS B:283 , ASP B:285 , HOH B:300 , HIS D:261BINDING SITE FOR RESIDUE ZN B 292
20CC2SOFTWAREASP B:68 , HIS B:71 , HIS B:75 , HOH B:296BINDING SITE FOR RESIDUE ZN B 293
21CC3SOFTWAREHIS B:232 , HIS B:248 , ASP B:285 , HOH B:295 , HOH B:300BINDING SITE FOR RESIDUE ZN B 294
22CC4SOFTWAREASP D:45 , ASP D:49 , HIS D:153 , ASP D:157BINDING SITE FOR RESIDUE ZN D 293

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H90)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3H90)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H90)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H90)

(-) Exons   (0, 0)

(no "Exon" information available for 3H90)

(-) 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:283
 aligned with FIEF_ECOLI | P69380 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:283
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287   
           FIEF_ECOLI     8 LVSRAAIAATAMASLLLLIKIFAWWYTGSVSILAALVDSLVDIGASLTNLLVVRYSLQPADDNHSFGHGKAESLAALAQSMFISGSALFLFLTGIQHLISPTPMTDPGVGVIVTIVALICTIILVSFQRWVVRRTQSQAVRADMLHYQSDVMMNGAILLALGLSWYGWHRADALFALGIGIYILYSALRMGYEAVQSLLDRALPDEERQEIIDIVTSWPGVSGAHDLRTRQSGPTRFIQIHLEMEDSLPLVQAHMVADQVEQAILRRFPGSDVIIHQDPCSVV 290
               SCOP domains d3h90a1 A:8-208 automated matches                                                                                                                                                                        d3h90a2 A:209-290 automated matches                                                SCOP domains
               CATH domains 3h90A01 A:8-206 Cation efflux protein cytoplasmic domain-like                                                                                                                                          3h90A02 A:207-290 Cation efflux protein cytoplasmic domain-like                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh....eeeeeeeeee..eeeeeeeee.....hhhhhhhhhhhhhhhhhhhh...eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h90 A   8 LVSRAAIAATAMASLLLLIKIFAWWYTGSVSILAALVDSLVDIGASLTNLLVVRYSLQPADDNHSFGHGKAESLAALAQSMFISGSALFLFLTGIQHLISPTPMTDPGVGVIVTIVALICTIILVSFQRWVVRRTQSQAVRADMLHYQSDVMMNGAILLALGLSWYGWHRADALFALGIGIYILYSALRMGYEAVQSLLDRALPDEERQEIIDIVTSWPGVSGAHDLRTRQSGPTRFIQIHLEMEDSLPLVQAHMVADQVEQAILRRFPGSDVIIHQDPCSVV 290
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287   

Chain B from PDB  Type:PROTEIN  Length:283
 aligned with FIEF_ECOLI | P69380 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:283
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287   
           FIEF_ECOLI     8 LVSRAAIAATAMASLLLLIKIFAWWYTGSVSILAALVDSLVDIGASLTNLLVVRYSLQPADDNHSFGHGKAESLAALAQSMFISGSALFLFLTGIQHLISPTPMTDPGVGVIVTIVALICTIILVSFQRWVVRRTQSQAVRADMLHYQSDVMMNGAILLALGLSWYGWHRADALFALGIGIYILYSALRMGYEAVQSLLDRALPDEERQEIIDIVTSWPGVSGAHDLRTRQSGPTRFIQIHLEMEDSLPLVQAHMVADQVEQAILRRFPGSDVIIHQDPCSVV 290
               SCOP domains d3h90b1 B:8-208 automated matches                                                                                                                                                                        d3h90b2 B:209-290 automated matches                                                SCOP domains
               CATH domains 3h90B01 B:8-206 Cation efflux protein cytoplasmic domain-like                                                                                                                                          3h90B02 B:207-290 Cation efflux protein cytoplasmic domain-like                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh....eeeeeeeeee..eeeeeeeee.....hhhhhhhhhhhhhhhhhhhh...eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h90 B   8 LVSRAAIAATAMASLLLLIKIFAWWYTGSVSILAALVDSLVDIGASLTNLLVVRYSLQPADDNHSFGHGKAESLAALAQSMFISGSALFLFLTGIQHLISPTPMTDPGVGVIVTIVALICTIILVSFQRWVVRRTQSQAVRADMLHYQSDVMMNGAILLALGLSWYGWHRADALFALGIGIYILYSALRMGYEAVQSLLDRALPDEERQEIIDIVTSWPGVSGAHDLRTRQSGPTRFIQIHLEMEDSLPLVQAHMVADQVEQAILRRFPGSDVIIHQDPCSVV 290
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287   

Chain C from PDB  Type:PROTEIN  Length:283
 aligned with FIEF_ECOLI | P69380 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:283
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287   
           FIEF_ECOLI     8 LVSRAAIAATAMASLLLLIKIFAWWYTGSVSILAALVDSLVDIGASLTNLLVVRYSLQPADDNHSFGHGKAESLAALAQSMFISGSALFLFLTGIQHLISPTPMTDPGVGVIVTIVALICTIILVSFQRWVVRRTQSQAVRADMLHYQSDVMMNGAILLALGLSWYGWHRADALFALGIGIYILYSALRMGYEAVQSLLDRALPDEERQEIIDIVTSWPGVSGAHDLRTRQSGPTRFIQIHLEMEDSLPLVQAHMVADQVEQAILRRFPGSDVIIHQDPCSVV 290
               SCOP domains d3h90c1 C:8-208 automated matches                                                                                                                                                                        d3h90c2 C:209-290 automated matches                                                SCOP domains
               CATH domains 3h90C01 C:8-206 Cation efflux protein cytoplasmic domain-like                                                                                                                                          3h90C02 C:207-290 Cation efflux protein cytoplasmic domain-like                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh....eeeeeeeeee..eeeeeeeee.....hhhhhhhhhhhhhhhhhhhh...eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h90 C   8 LVSRAAIAATAMASLLLLIKIFAWWYTGSVSILAALVDSLVDIGASLTNLLVVRYSLQPADDNHSFGHGKAESLAALAQSMFISGSALFLFLTGIQHLISPTPMTDPGVGVIVTIVALICTIILVSFQRWVVRRTQSQAVRADMLHYQSDVMMNGAILLALGLSWYGWHRADALFALGIGIYILYSALRMGYEAVQSLLDRALPDEERQEIIDIVTSWPGVSGAHDLRTRQSGPTRFIQIHLEMEDSLPLVQAHMVADQVEQAILRRFPGSDVIIHQDPCSVV 290
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287   

Chain D from PDB  Type:PROTEIN  Length:283
 aligned with FIEF_ECOLI | P69380 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:283
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287   
           FIEF_ECOLI     8 LVSRAAIAATAMASLLLLIKIFAWWYTGSVSILAALVDSLVDIGASLTNLLVVRYSLQPADDNHSFGHGKAESLAALAQSMFISGSALFLFLTGIQHLISPTPMTDPGVGVIVTIVALICTIILVSFQRWVVRRTQSQAVRADMLHYQSDVMMNGAILLALGLSWYGWHRADALFALGIGIYILYSALRMGYEAVQSLLDRALPDEERQEIIDIVTSWPGVSGAHDLRTRQSGPTRFIQIHLEMEDSLPLVQAHMVADQVEQAILRRFPGSDVIIHQDPCSVV 290
               SCOP domains d3h90d1 D:8-208 automated matches                                                                                                                                                                        d3h90d2 D:209-290 automated matches                                                SCOP domains
               CATH domains 3h90D01 D:8-206 Cation efflux protein cytoplasmic domain-like                                                                                                                                          3h90D02 D:207-290 Cation efflux protein cytoplasmic domain-like                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh....eeeeeeeeee..eeeeeeeee.....hhhhhhhhhhhhhhhhhhhh...eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h90 D   8 LVSRAAIAATAMASLLLLIKIFAWWYTGSVSILAALVDSLVDIGASLTNLLVVRYSLQPADDNHSFGHGKAESLAALAQSMFISGSALFLFLTGIQHLISPTPMTDPGVGVIVTIVALICTIILVSFQRWVVRRTQSQAVRADMLHYQSDVMMNGAILLALGLSWYGWHRADALFALGIGIYILYSALRMGYEAVQSLLDRALPDEERQEIIDIVTSWPGVSGAHDLRTRQSGPTRFIQIHLEMEDSLPLVQAHMVADQVEQAILRRFPGSDVIIHQDPCSVV 290
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287   

   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, 8)

Asymmetric Unit

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H90)

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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

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

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        FIEF_ECOLI | P693802qfi

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