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(-) Description

Title :  NITRATE-BOUND D85S MUTANT OF BACTERIORHODOPSIN
 
Authors :  M. T. Facciotti, V. S. Cheung, C. S. Lunde, S. Rouhani, N. S. Baliga, R. M. Glaeser
Date :  02 Feb 04  (Deposition) - 08 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Bacteriorhodopsin, Anion, Pump, X-Ray Diffraction, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. T. Facciotti, V. S. Cheung, C. S. Lunde, S. Rouhani, N. S. Baliga, R. M. Glaeser
Specificity Of Anion Binding In The Substrate Pocket Of Bacteriorhodopsin.
Biochemistry V. 43 4934 2004
PubMed-ID: 15109251  |  Reference-DOI: 10.1021/BI035757S
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BACTERIORHODOPSIN PRECURSOR
    Chains: A
    Engineered: YES
    Expression System: HALOBACTERIUM SP. NRC-1
    Expression System Taxid: 64091
    Gene: BOP, VNG1467G
    Mutation: YES
    Organism Scientific: HALOBACTERIUM SP.
    Organism Taxid: 2243
    Synonym: BR

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1LI17Ligand/Ion1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL
2NO31Ligand/IonNITRATE ION
3RET1Ligand/IonRETINAL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:57 , SER A:85 , TRP A:86 , ASP A:212 , LYS A:216 , RET A:301 , HOH A:402BINDING SITE FOR RESIDUE NO3 A 801
2AC2SOFTWARETRP A:86 , THR A:89 , THR A:90 , MET A:118 , SER A:141 , THR A:142 , TRP A:182 , TYR A:185 , PRO A:186 , TRP A:189 , ASP A:212 , LYS A:216 , NO3 A:801BINDING SITE FOR RESIDUE RET A 301
3AC3SOFTWAREPRO A:91 , GLN A:105 , ILE A:108 , VAL A:199 , ILE A:203BINDING SITE FOR RESIDUE LI1 A 601
4AC4SOFTWAREMET A:56BINDING SITE FOR RESIDUE LI1 A 602
5AC5SOFTWAREPHE A:135BINDING SITE FOR RESIDUE LI1 A 605
6AC6SOFTWAREALA A:143BINDING SITE FOR RESIDUE LI1 A 606
7AC7SOFTWARETHR A:5 , LEU A:15 , ASN A:202 , ILE A:203BINDING SITE FOR RESIDUE LI1 A 608

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S8J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S8J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S8J)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BACTERIAL_OPSIN_1PS00950 Bacterial rhodopsins signature 1.BACR_HALSA95-107  1A:82-94
2BACTERIAL_OPSIN_RETPS00327 Bacterial rhodopsins retinal binding site.BACR_HALSA221-232  1A:208-219

(-) Exons   (0, 0)

(no "Exon" information available for 1S8J)

(-) 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:216
 aligned with BACR_HALSA | P02945 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:229
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236         
           BACR_HALSA    17 ITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGE 245
               SCOP domains d1s8ja_ A: Bacteriorhodopsin                                                                                                                                                                                                          SCOP domains
               CATH domains 1s8jA00 A:4-232 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                             CATH domains
               Pfam domains ------Bac_rhodopsin-1s8jA01 A:10-232                                                                                                                                                                                                  Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh-------------.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------BACTERIAL_OPS-----------------------------------------------------------------------------------------------------------------BACTERIAL_OP------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s8j A   4 ITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGY-------------IYWARYASWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGE 232
                                    13        23        33        43        53        63|        -    |   83        93       103       113       123       133       143       153       163       173       183       193       203       213       223         
                                                                                       64            78
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BACR_HALSA | P02945)
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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  1s8j
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  BACR_HALSA | P02945
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 Related Entries

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

UniProtKB/Swiss-Prot
        BACR_HALSA | P02945: 1ap9 1at9 1bac 1bad 1bct 1bha 1bhb 1bm1 1brd 1brr 1brx 1c3w 1c8r 1c8s 1cwq 1dze 1e0p 1f4z 1f50 1fbb 1fbk 1iw6 1iw9 1ixf 1jv6 1jv7 1kg8 1kg9 1kgb 1kme 1l0m 1m0k 1m0l 1m0m 1mgy 1o0a 1p8h 1p8i 1p8u 1pxr 1pxs 1py6 1q5i 1q5j 1qhj 1qko 1qkp 1qm8 1r2n 1r84 1s51 1s52 1s53 1s54 1s8l 1tn0 1tn5 1ucq 1vjm 1x0i 1x0k 1x0s 1xji 2at9 2brd 2i1x 2i20 2i21 2ntu 2ntw 2wjk 2wjl 2zfe 2zzl 3coc 3cod 3han 3hao 3hap 3haq 3har 3has 3mbv 3ns0 3nsb 3t45 3utv 3utw 3utx 3uty 3vhz 3vi0 4fpd 4hwl 4hyx 4md1 4md2 4ov0 4x31 4x32 4xxj 5a44 5a45 5b34 5b35 5b6v 5b6w 5b6x 5b6y 5b6z 5br2 5br5 5h2h 5h2i 5h2j 5h2k 5h2l 5h2m 5h2n 5h2o 5h2p 5j7a 5vn7 5vn9

(-) Related Entries Specified in the PDB File

1mgy BROMIDE-BOUND D85S MUTANT
1s8l ANION-FREE FORM OF THE D85S MUTANT OF BACTERIORHODOPSIN FROM CRYSTALS GROWN IN THE PRESENCE OF HALIDE