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(-) Description

Title :  CRYSTAL STRUCTURE OF ARCHAERHODOPSIN-2
 
Authors :  K. Yoshimura, N. Enami, M. Murakami, H. Okumura, K. Ihara, T. Kouyama
Date :  28 Apr 04  (Deposition) - 04 Oct 05  (Release) - 10 Jun 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Retinal-Binding Protein, Proton Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Enami, K. Yoshimura, M. Murakami, H. Okumura, K. Ihara, T. Kouyama
Crystal Structures Of Archaerhodopsin-1 And -2: Common Structural Motif In Archaeal Light-Driven Proton Pumps
J. Mol. Biol. V. 358 675 2006
PubMed-ID: 16540121  |  Reference-DOI: 10.1016/J.JMB.2006.02.032
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ARCHAERHODOPSIN 2
    Chains: A, B
    Organism Scientific: HALOBACTERIUM SP.
    Organism Taxid: 29285
    Strain: AUS-2
    Synonym: AR 2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric/Biological Unit (3, 17)
No.NameCountTypeFull Name
1BNG12Ligand/IonB-NONYLGLUCOSIDE
2RET2Ligand/IonRETINAL
3SO43Ligand/IonSULFATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:110 , GLY A:114 , LEU A:132 , TRP A:142BINDING SITE FOR RESIDUE BNG A 301
02AC2SOFTWAREPRO A:136 , TYR A:140 , BNG A:303BINDING SITE FOR RESIDUE BNG A 302
03AC3SOFTWARETYR A:155 , BNG A:302BINDING SITE FOR RESIDUE BNG A 303
04AC4SOFTWARETYR A:140 , ILE A:195 , GLY A:200 , BNG A:305BINDING SITE FOR RESIDUE BNG A 304
05AC5SOFTWARELEU A:151 , BNG A:304 , PHE B:152 , TYR B:155BINDING SITE FOR RESIDUE BNG A 305
06AC6SOFTWAREVAL A:185 , ILE A:208 , BNG A:307 , BNG A:308BINDING SITE FOR RESIDUE BNG A 306
07AC7SOFTWAREBNG A:306 , LEU B:158 , ALA B:184BINDING SITE FOR RESIDUE BNG A 307
08AC8SOFTWARETRP A:16 , BNG A:306BINDING SITE FOR RESIDUE BNG A 308
09AC9SOFTWAREILE A:68 , TYR A:85BINDING SITE FOR RESIDUE BNG A 309
10BC1SOFTWAREARG A:168 , SER A:169 , VAL A:172 , ARG B:232BINDING SITE FOR RESIDUE SO4 A 400
11BC2SOFTWARETRP A:91 , THR A:94 , THR A:95 , MET A:123 , TRP A:143 , SER A:146 , THR A:147 , TRP A:187 , TYR A:190 , PRO A:191 , TRP A:194 , ASP A:217 , LYS A:221BINDING SITE FOR RESIDUE RET A 260
12BC3SOFTWARETHR B:115 , VAL B:119 , TYR B:156BINDING SITE FOR RESIDUE BNG B 310
13BC4SOFTWAREALA A:48 , TRP B:36BINDING SITE FOR RESIDUE BNG B 311
14BC5SOFTWAREARG A:162 , ASN A:177 , LEU B:75 , SER B:77 , THR B:79 , PRO B:136 , ARG B:139 , TYR B:140 , ILE B:195 , GLY B:200 , ALA B:201BINDING SITE FOR RESIDUE BNG B 312
15BC6SOFTWAREARG A:232 , ARG B:168 , SER B:169 , VAL B:172 , HOH B:700 , HOH B:704 , HOH B:708BINDING SITE FOR RESIDUE SO4 B 401
16BC7SOFTWAREVAL A:38 , ARG A:44 , HOH A:701 , TRP B:36 , VAL B:38 , THR B:39 , ARG B:44BINDING SITE FOR RESIDUE SO4 B 402
17BC8SOFTWARETRP B:91 , THR B:94 , THR B:95 , TRP B:143 , SER B:146 , TRP B:187 , TYR B:190 , PRO B:191 , ASP B:217 , LYS B:221BINDING SITE FOR RESIDUE RET B 261

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VGO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VGO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VGO)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BACTERIAL_OPSIN_1PS00950 Bacterial rhodopsins signature 1.BACR2_HALS293-105
 		  2A:87-99
B:87-99
2BACTERIAL_OPSIN_RETPS00327 Bacterial rhodopsins retinal binding site.BACR2_HALS2219-230
 		  2A:213-224
B:213-224

(-) Exons   (0, 0)

(no "Exon" information available for 1VGO)

(-) 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:233
 aligned with BACR2_HALS2 | P29563 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:233
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
          BACR2_HALS2    11 DLLNDGRPETLWLGIGTLLMLIGTFYFIARGWGVTDKEAREYYAITILVPGIASAAYLAMFFGIGVTEVELASGTVLDIYYARYADWLFTTPLLLLDLALLAKVDRVTIGTLIGVDALMIVTGLIGALSKTPLARYTWWLFSTIAFLFVLYYLLTSLRSAAAKRSEEVRSTFNTLTALVAVLWTAYPILWIVGTEGAGVVGLGIETLAFMVLDVTAKVGFGFVLLRSRAILGE 243
               SCOP domains d1vgoa_ A: automated matches                                                                                                                                                                                                              SCOP domains
               CATH domains 1vgoA00 A:5-237 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.....eeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------BACTERIAL_OPS-----------------------------------------------------------------------------------------------------------------BACTERIAL_OP------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vgo A   5 DLLNDGRPETLWLGIGTLLMLIGTFYFIARGWGVTDKEAREYYAITILVPGIASAAYLAMFFGIGVTEVELASGTVLDIYYARYADWLFTTPLLLLDLALLAKVDRVTIGTLIGVDALMIVTGLIGALSKTPLARYTWWLFSTIAFLFVLYYLLTSLRSAAAKRSEEVRSTFNTLTALVAVLWTAYPILWIVGTEGAGVVGLGIETLAFMVLDVTAKVGFGFVLLRSRAILGE 237
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234   


Chain B from PDB  Type:PROTEIN  Length:235
 aligned with BACR2_HALS2 | P29563 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:235
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
          BACR2_HALS2    11 DLLNDGRPETLWLGIGTLLMLIGTFYFIARGWGVTDKEAREYYAITILVPGIASAAYLAMFFGIGVTEVELASGTVLDIYYARYADWLFTTPLLLLDLALLAKVDRVTIGTLIGVDALMIVTGLIGALSKTPLARYTWWLFSTIAFLFVLYYLLTSLRSAAAKRSEEVRSTFNTLTALVAVLWTAYPILWIVGTEGAGVVGLGIETLAFMVLDVTAKVGFGFVLLRSRAILGETE 245
               SCOP domains d1vgob_ B: automated matches                                                                                                                                                                                                                SCOP domains
               CATH domains 1vgoB00 B:5-239 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                                   CATH domains
           Pfam domains (1) ---------Bac_rhodopsin-1vgoB01 B:14-239                                                                                                                                                                                                     Pfam domains (1)
           Pfam domains (2) ---------Bac_rhodopsin-1vgoB02 B:14-239                                                                                                                                                                                                     Pfam domains (2)
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.....eeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------BACTERIAL_OPS-----------------------------------------------------------------------------------------------------------------BACTERIAL_OP--------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vgo B   5 DLLNDGRPETLWLGIGTLLMLIGTFYFIARGWGVTDKEAREYYAITILVPGIASAAYLAMFFGIGVTEVELASGTVLDIYYARYADWLFTTPLLLLDLALLAKVDRVTIGTLIGVDALMIVTGLIGALSKTPLARYTWWLFSTIAFLFVLYYLLTSLRSAAAKRSEEVRSTFNTLTALVAVLWTAYPILWIVGTEGAGVVGLGIETLAFMVLDVTAKVGFGFVLLRSRAILGETE 239
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: GPCR_A (90)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BACR2_HALS2 | P29563)
molecular function
    GO:0005216    ion channel activity    Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
    GO:0009881    photoreceptor activity    The function of absorbing and responding to incidental electromagnetic radiation, particularly visible light. The response may involve a change in conformation.
biological process
    GO:0034220    ion transmembrane transport    A process in which an ion is transported from one side of a membrane to the other 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:0007602    phototransduction    The sequence of reactions within a cell required to convert absorbed photons into a molecular signal.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
    GO:0015992    proton transport    The directed movement of protons (hydrogen ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0050896    response to stimulus    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 stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
    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: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)

UniProtKB/Swiss-Prot
        BACR2_HALS2 | P29563: 2ei4 2z55 3wqj

(-) Related Entries Specified in the PDB File

1uaz CRYSTAL STRUCTURE OF ARCHAERHODOPSIN-1