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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DESULFOVIBRO VULGARIS UREA TRANSPORTER IN THE P3(1) SPACE GROUP AT 3.86
 
Authors :  E. J. Levin, M. Zhou, New York Consortium On Membrane Protein Str (Nycomps)
Date :  31 Mar 10  (Deposition) - 19 Jan 11  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.86
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Membrane Protein, Channel, Structural Genomics, Psi-2, Protein Structure Initiative, New York Consortium On Membrane Protein Structure, Nycomps, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. J. Levin, M. Zhou
Crystal Structure Of The Desulfovibro Vulgaris Urea Transporter In The P3(1) Space Group At 3. 86 .
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UREA TRANSPORTER
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DVU_1160
    Organism Scientific: DESULFOVIBRIO VULGARIS
    Organism Taxid: 882
    Strain: HILDENBOROUGH

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3ME1)

(-) Sites  (0, 0)

(no "Site" information available for 3ME1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ME1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ME1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ME1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ME1)

(-) Exons   (0, 0)

(no "Exon" information available for 3ME1)

(-) 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:321
 aligned with UT_DESVH | Q72CX3 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:325
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329     
             UT_DESVH    10 PLIEFCDSVCRGCGQVMFQNNTVTGLLFFAGIFYNSTTLGVCAVLGTAASTLTAQLLGVDKPLVRAGLFGFNGTLAGIALPFFFNYEPAMLGYVALNGAFTTIIMASLLNFLGKWGVPALTAPFVLATWLLMFGVYKLSLFHPGALIAPALPSVAGLADMGTVTGRTFMEGLFKGVGEVMFQDNIVTGVIFVVAILVNSRISALFAVIGSLVGLCTALIMHSPETPVRLGLYGFNSVLCGIAMGGIFFYLNIRTFLYALGCMVLGAIATGAFSVLLSPIGMPALTWPFIVVTWLFLFAGSMFRNIAQVPTEKAGTPEDNLRSLAI 334
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh................----.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh........hhhhh...hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3me1 A  10 PLIEFCDSVCRGCGQVMFQNNTVTGLLFFAGIFYNSTTLGVCAVLGTAASTLTAQLLGVDKPLVRAGLFGFNGTLAGIALPFFFNYEPAMLGYVALNGAFTTIIMASLLNFLGKWGVPALTAPFVLATWLLMFGVYKLSLFHPGALIAPALPSV----DMGTVTGRTFMEGLFKGVGEVMFQDNIVTGVIFVVAILVNSRISALFAVIGSLVGLCTALIMHSPETPVRLGLYGFNSVLCGIAMGGIFFYLNIRTFLYALGCMVLGAIATGAFSVLLSPIGMPALTWPFIVVTWLFLFAGSMFRNIAQVPTEKAGTPEDNLRSLAI 334
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159   |   169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329     
                                                                                                                                                                                   163  168                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:323
 aligned with UT_DESVH | Q72CX3 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:327
                                    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       297       307       317       327       
             UT_DESVH     8 KNPLIEFCDSVCRGCGQVMFQNNTVTGLLFFAGIFYNSTTLGVCAVLGTAASTLTAQLLGVDKPLVRAGLFGFNGTLAGIALPFFFNYEPAMLGYVALNGAFTTIIMASLLNFLGKWGVPALTAPFVLATWLLMFGVYKLSLFHPGALIAPALPSVAGLADMGTVTGRTFMEGLFKGVGEVMFQDNIVTGVIFVVAILVNSRISALFAVIGSLVGLCTALIMHSPETPVRLGLYGFNSVLCGIAMGGIFFYLNIRTFLYALGCMVLGAIATGAFSVLLSPIGMPALTWPFIVVTWLFLFAGSMFRNIAQVPTEKAGTPEDNLRSLAI 334
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh................----.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh........hhhhh...hhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3me1 B   8 KNPLIEFCDSVCRGCGQVMFQNNTVTGLLFFAGIFYNSTTLGVCAVLGTAASTLTAQLLGVDKPLVRAGLFGFNGTLAGIALPFFFNYEPAMLGYVALNGAFTTIIMASLLNFLGKWGVPALTAPFVLATWLLMFGVYKLSLFHPGALIAPALPSV----DMGTVTGRTFMEGLFKGVGEVMFQDNIVTGVIFVVAILVNSRISALFAVIGSLVGLCTALIMHSPETPVRLGLYGFNSVLCGIAMGGIFFYLNIRTFLYALGCMVLGAIATGAFSVLLSPIGMPALTWPFIVVTWLFLFAGSMFRNIAQVPTEKAGTPEDNLRSLAI 334
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157     |   -|      177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       
                                                                                                                                                                                     163  168                                                                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:312
 aligned with UT_DESVH | Q72CX3 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:325
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329     
             UT_DESVH    10 PLIEFCDSVCRGCGQVMFQNNTVTGLLFFAGIFYNSTTLGVCAVLGTAASTLTAQLLGVDKPLVRAGLFGFNGTLAGIALPFFFNYEPAMLGYVALNGAFTTIIMASLLNFLGKWGVPALTAPFVLATWLLMFGVYKLSLFHPGALIAPALPSVAGLADMGTVTGRTFMEGLFKGVGEVMFQDNIVTGVIFVVAILVNSRISALFAVIGSLVGLCTALIMHSPETPVRLGLYGFNSVLCGIAMGGIFFYLNIRTFLYALGCMVLGAIATGAFSVLLSPIGMPALTWPFIVVTWLFLFAGSMFRNIAQVPTEKAGTPEDNLRSLAI 334
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh-.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhh...hhhhhhhhhhhhhh--..hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..................----------.hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh........hhhhh...hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3me1 C  10 PLIEFCDSVCRGCGQVMFQNNTVTGLLFFAGIF-NSTTLGVCAVLGTAASTLTAQLLGVDKPLVRAGLFGFNGTLAGIALPFF--YEPAMLGYVALNGAFTTIIMASLLNFLGKWGVPALTAPFVLATWLLMFGVYKLSLFHPGALIAPALPSVAG----------TFMEGLFKGVGEVMFQDNIVTGVIFVVAILVNSRISALFAVIGSLVGLCTALIMHSPETPVRLGLYGFNSVLCGIAMGGIFFYLNIRTFLYALGCMVLGAIATGAFSVLLSPIGMPALTWPFIVVTWLFLFAGSMFRNIAQVPTEKAGTPEDNLRSLAI 334
                                    19        29        39  | |   49        59        69        79        89  |  |  99       109       119       129       139       149       159     |   -      |179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329     
                                                           42 |                                              92 95                                                                   165        176                                                                                                                                                              
                                                             44
   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 3ME1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ME1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ME1)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (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: 3k3f 3k3g 3m6e

(-) Related Entries Specified in the PDB File

3k3f