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(-) Description

Title :  CRYSTAL STRUCTURE OF THE UREA TRANSPORTER FROM DESULFOVIBRIO VULGARIS
 
Authors :  E. J. Levin, M. Zhou, New York Consortium On Membrane Protein Str (Nycomps)
Date :  02 Oct 09  (Deposition) - 17 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Membrane Protein, Channel, Urea Transport, Transporter, Transport Protein, Structural Genomics, Psi-2, Protein Structure Initiative, New York Consortium On Membrane Protein Structure, Nycomps (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. J. Levin, M. Quick, M. Zhou
Crystal Structure Of A Bacterial Homologue Of The Kidney Urea Transporter.
Nature V. 462 757 2009
PubMed-ID: 19865084  |  Reference-DOI: 10.1038/NATURE08558

(-) Compounds

Molecule 1 - UREA TRANSPORTER
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DVU_1160
    Organism Scientific: DESULFOVIBRIO VULGARIS
    Organism Taxid: 882
    Strain: HILDENBOROUGH

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric Unit (1, 9)
No.NameCountTypeFull Name
1AU9Ligand/IonGOLD ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1AU-1Ligand/IonGOLD ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:24BINDING SITE FOR RESIDUE AU A 338
2AC2SOFTWARECYS A:19 , THR A:31 , AU A:340 , AU A:345BINDING SITE FOR RESIDUE AU A 339
3AC3SOFTWARECYS A:15 , CYS A:19 , AU A:339 , AU A:345 , AU A:346BINDING SITE FOR RESIDUE AU A 340
4AC4SOFTWARETHR A:47 , VAL A:50 , CYS A:51 , LEU A:100 , AU A:343BINDING SITE FOR RESIDUE AU A 341
5AC5SOFTWARECYS A:224 , AU A:344BINDING SITE FOR RESIDUE AU A 342
6AC6SOFTWARECYS A:51 , PRO A:90 , AU A:341BINDING SITE FOR RESIDUE AU A 343
7AC7SOFTWARECYS A:224 , AU A:342BINDING SITE FOR RESIDUE AU A 344
8AC8SOFTWARECYS A:15 , ASP A:16 , AU A:339 , AU A:340 , AU A:346BINDING SITE FOR RESIDUE AU A 345
9AC9SOFTWARECYS A:15 , AU A:340 , AU A:345BINDING SITE FOR RESIDUE AU A 346

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K3F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3K3F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K3F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K3F)

(-) Exons   (0, 0)

(no "Exon" information available for 3K3F)

(-) 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:332
 aligned with UT_DESVH | Q72CX3 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:336
                              1                                                                                                                                                                                                                                                                                                                                             
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328      
             UT_DESVH     - --MFGEQLLKNPLIEFCDSVCRGCGQVMFQNNTVTGLLFFAGIFYNSTTLGVCAVLGTAASTLTAQLLGVDKPLVRAGLFGFNGTLAGIALPFFFNYEPAMLGYVALNGAFTTIIMASLLNFLGKWGVPALTAPFVLATWLLMFGVYKLSLFHPGALIAPALPSVAGLADMGTVTGRTFMEGLFKGVGEVMFQDNIVTGVIFVVAILVNSRISALFAVIGSLVGLCTALIMHSPETPVRLGLYGFNSVLCGIAMGGIFFYLNIRTFLYALGCMVLGAIATGAFSVLLSPIGMPALTWPFIVVTWLFLFAGSMFRNIAQVPTEKAGTPEDNLRSLAI 334
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3k3fA00 A:-1-334 Ammonium transporter AmtB like domains                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.................----.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh...hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..............hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3k3f A  -1 GRAFGEQLLKNPLIEFCDSVCRGCGQVMFQNNTVTGLLFFAGIFYNSTTLGVCAVLGTAASTLTAQLLGVDKPLVRAGLFGFNGTLAGIALPFFFNYEPAMLGYVALNGAFTTIIMASLLNFLGKWGVPALTAPFVLATWLLMFGVYKLSLFHPGALIAPALPSV----DMGTVTGRTFMEGLFKGVGEVMFQDNIVTGVIFVVAILVNSRISALFAVIGSLVGLCTALIMHSPETPVRLGLYGFNSVLCGIAMGGIFFYLNIRTFLYALGCMVLGAIATGAFSVLLSPIGMPALTWPFIVVTWLFLFAGSMFRNIAQVPTEKAGTPEDNLRSLAI 334
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158    |  168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328      
                                                                                                                                                                                              163  168
   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)
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  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 3K3F)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3K3F)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (UT_DESVH | Q72CX3)
molecular function
    GO:0033219    urea binding    Interacting selectively and non-covalently with urea, a water-soluble carboxamide with the structure H2N-CO-NH2.
    GO:0015265    urea channel activity    Enables the facilitated diffusion of urea (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
    GO:0015204    urea transmembrane transporter activity    Enables the directed movement of urea cross a membrane into, out of or within a cell, or between cells. Urea is the water soluble compound H2N-CO-NH2.
biological process
    GO:0070207    protein homotrimerization    The formation of a protein homotrimer, a macromolecular structure consisting of three noncovalently associated identical subunits.
    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:0071918    urea transmembrane transport    The process in which urea, the water-soluble compound H2N-CO-NH2, is transported from one side of a membrane to the other 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:0031226    intrinsic component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in 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)

UniProtKB/Swiss-Prot
        UT_DESVH | Q72CX3: 3k3g 3m6e 3me1

(-) Related Entries Specified in the PDB File

3k3g CRYSTAL STRUCTURE OF THE UREA TRANSPORTER FROM DESULFOVIBRIO VULGARIS BOUND TO N,N,-DIMETHYLUREA RELATED ID: GO.3782 RELATED DB: TARGETDB