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(-) Description

Title :  BACTERIORHODOPSIN MUTANT E204D
 
Authors :  M. Potschies, E. Hofmann, K. Gerwert
Date :  27 May 09  (Deposition) - 25 Aug 10  (Release) - 06 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Proton Transport, Ion Pump, Retinal Protein, Photoreceptor Protein, Hydrogen Ion Transport, Pyrrolidone, Merohedral Twinning, Sensory Transduction, Serpentine, Chromophore, Photoreceptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Wolf, E. Freier, M. Potschies, E. Hofmann, K. Gerwert
Directional Proton Transfer In Membrane Proteins Achieved Through Protonated Protein-Bound Water Molecules: A Proton Diode.
Angew. Chem. Int. Ed. Engl. V. 49 6889 2010
PubMed-ID: 20680951  |  Reference-DOI: 10.1002/ANIE.201001243

(-) Compounds

Molecule 1 - BACTERIORHODOPSIN
    Chains: A
    Mutation: YES
    Organism Scientific: HALOBACTERIUM SALINARUM
    Organism Taxid: 2242
    Other Details: RETINAL LINKED VIA SCHIFF BASE TO K216
    Synonym: BR

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1LI11Ligand/Ion1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL
2RET1Ligand/IonRETINAL
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1LI13Ligand/Ion1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL
2RET3Ligand/IonRETINAL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:86 , THR A:89 , THR A:90 , MET A:118 , TRP A:138 , SER A:141 , TRP A:182 , TYR A:185 , TRP A:189 , ASP A:212 , LYS A:216BINDING SITE FOR RESIDUE RET A 301
2AC2SOFTWARETHR A:24 , LEU A:28 , TYR A:43 , ALA A:44 , THR A:47 , ALA A:51 , PHE A:54 , ALA A:144 , TYR A:147BINDING SITE FOR RESIDUE LI1 A1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WJK)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Met A:32 -Gly A:33

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WJK)

(-) PROSITE Motifs  (2, 2)

Asymmetric 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
Biological Unit 1 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BACTERIAL_OPSIN_1PS00950 Bacterial rhodopsins signature 1.BACR_HALSA95-107  3A:82-94
2BACTERIAL_OPSIN_RETPS00327 Bacterial rhodopsins retinal binding site.BACR_HALSA221-232  3A:208-219

(-) Exons   (0, 0)

(no "Exon" information available for 2WJK)

(-) 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:210
 aligned with BACR_HALSA | P02945 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:227
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       
           BACR_HALSA    18 TGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG 244
               SCOP domains d2wjka_ A: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains 2wjkA00 A:5-231 Rhopdopsin 7-    helix transmembrane proteins                                                                                                                                                                       CATH domains
               Pfam domains -----Bac_rhodopsin-2wjkA01 A:    10-231                                                                                                                                                                                             Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhh..----hhhhhhhhhhhhhhhhhhhhhhhhh...eeee..---.eeeehhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh----------hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------BACTERIAL_OPS-----------------------------------------------------------------------------------------------------------------BACTERIAL_OP------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wjk A   5 TGRPEWIWLALGTALMGLGTLYFLVKGMG----DAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPF---QNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFG----------EVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIDTLLFMVLDVSAKVGFGLILLRSRAIFG 231
                                    14        24        |-   |    44        54        64      |  -|       84        94       104       114       124       134       144       154|        - |     174       184       194       204       214       224       
                                                       33   38                               71  75                                                                             155        166
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: GPCR_A (90)

(-) Gene Ontology  (12, 12)

Asymmetric 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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  2wjk
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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 1s8j 1s8l 1tn0 1tn5 1ucq 1vjm 1x0i 1x0k 1x0s 1xji 2at9 2brd 2i1x 2i20 2i21 2ntu 2ntw 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

1ap9 X-RAY STRUCTURE OF BACTERIORHODOPSIN FROM MICROCRYSTALS GROWN IN LIPIDIC CUBIC PHASES
1at9 STRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM DETERMINED BY ELECTRON CRYSTALLOGRAPHY
1bac RHODOPSIN (7-HELIX BUNDLE) COMPLEX WITH ALL -TRANS RETINAL (THEORETICAL MODEL)
1bad BACTERIORHODOPSIN (7-HELIX BUNDLE) WITH 13- CIS RETINAL (THEORETICAL MODEL)
1bct BACTERIORHODOPSIN (FRAGMENT 163-231) (NMR, 14 STRUCTURES)
1bha BACTERIORHODOPSIN (PROTEOLYTIC FRAGMENT 1 - 71 , SOLUBILIZED IN SDS MICELLES) (NMR, 12 STRUCTURES)
1bhb BACTERIORHODOPSIN (PROTEOLYTIC FRAGMENT 1 - 71 , SOLUBILIZED IN METHANOL-CHLOROFORM) (NMR, 12 STRUCTURES)
1bm1 CRYSTAL STRUCTURE OF BACTERIORHODOPSIN IN THE LIGHT-ADAPTED STATE
1brd BACTERIORHODOPSIN
1brr X-RAY STRUCTURE OF THE BACTERIORHODOPSIN TRIMER/LIPID COMPLEX
1brx BACTERIORHODOPSIN/LIPID COMPLEX
1c3w BACTERIORHODOPSIN/LIPID COMPLEX AT 1.55 A RESOLUTION
1c8r BACTERIORHODOPSIN D96M BR STATE AT 2.0 A RESOLUTION
1c8s BACTERIORHODOPSIN D96N LATE M STATE INTERMEDIATE
1cwq M INTERMEDIATE STRUCTURE OF THE WILD TYPE BACTERIORHODOPSIN IN COMBINATION WITH THE GROUND STATE STRUCTURE
1dze STRUCTURE OF THE M INTERMEDIATE OF BACTERIORHODOPSIN TRAPPED AT 100K
1e0p L INTERMEDIATE OF BACTERIORHODOPSIN
1f4z BACTERIORHODOPSIN - M PHOTOINTERMEDIATE STATE OF THE E204Q MUTANT AT 1.8 ANGSTROM RESOLUTION
1f50 BACTERIORHODOPSIN - BR STATE OF THE E204Q MUTANT AT 1.7 ANGSTROM RESOLUTION
1fbb CRYSTAL STRUCTURE OF NATIVE CONFORMATION OFBACTERIORHODOPSIN
1fbk CRYSTAL STRUCTURE OF CYTOPLASMICALLY OPEN CONFORMATION OFBACTERIORHODOPSIN
1iw6 CRYSTAL STRUCTURE OF THE GROUND STATE OF BACTERIORHODOPSIN
1iw9 CRYSTAL STRUCTURE OF THE M INTERMEDIATE OF BACTERIORHODOPSIN
1ixf CRYSTAL STRUCTURE OF THE K INTERMEDIATE OF BACTERIORHODOPSIN
1jv6 BACTERIORHODOPSIN D85S/F219L DOUBLE MUTANT AT 2.00 ANGSTROMRESOLUTION
1jv7 BACTERIORHODOPSIN O-LIKE INTERMEDIATE STATE OF THE D85SMUTANT AT 2.25 ANGSTROM RESOLUTION
1kg8 X-RAY STRUCTURE OF AN EARLY-M INTERMEDIATE OFBACTERIORHODOPSIN
1kg9 STRUCTURE OF A "MOCK-TRAPPED" EARLY-M INTERMEDIATE OFBACTERIORHOSOPSIN
1kgb STRUCTURE OF GROUND-STATE BACTERIORHODOPSIN
1kme CRYSTAL STRUCTURE OF BACTERIORHODOPSIN CRYSTALLIZED FROMBICELLES
1l0m SOLUTION STRUCTURE OF BACTERIORHODOPSIN
1m0k BACTERIORHODOPSIN K INTERMEDIATE AT 1.43 A RESOLUTION
1m0l BACTERIORHODOPSIN/LIPID COMPLEX AT 1.47 A RESOLUTION
1m0m BACTERIORHODOPSIN M1 INTERMEDIATE AT 1.43 A RESOLUTION
1mgy STRUCTURE OF THE D85S MUTANT OF BACTERIORHODOPSIN WITHBROMIDE BOUND
1o0a BACTERIORHODOPSIN L INTERMEDIATE AT 1.62 A RESOLUTION
1p8h BACTERIORHODOPSIN M1 INTERMEDIATE PRODUCED AT ROOMTEMPERATURE
1p8i F219L BACTERIORHODOPSIN MUTANT
1p8u BACTERIORHODOPSIN N' INTERMEDIATE AT 1.62 A RESOLUTION
1pxr STRUCTURE OF PRO50ALA MUTANT OF BACTERIORHODOPSIN
1pxs STRUCTURE OF MET56ALA MUTANT OF BACTERIORHODOPSIN
1py6 BACTERIORHODOPSIN CRYSTALLIZED FROM BICELLS
1q5i CRYSTAL STRUCTURE OF BACTERIORHODOPSIN MUTANT P186ACRYSTALLIZED FROM BICELLES
1q5j CRYSTAL STRUCTURE OF BACTERIORHODOPSIN MUTANT P91ACRYSTALLIZED FROM BICELLES
1qhj X-RAY STRUCTURE OF BACTERIORHODOPSIN GROWN IN LIPIDIC CUBIC PHASES
1qko HIGH RESOLUTION X-RAY STRUCTURE OF AN EARLY INTERMEDIATE IN THE BACTERIORHODOPSIN PHOTOCYCLE
1qkp HIGH RESOLUTION X-RAY STRUCTURE OF AN EARLY INTERMEDIATE IN THE BACTERIORHODOPSIN PHOTOCYCLE
1qm8 STRUCTURE OF BACTERIORHODOPSIN AT 100 K
1r2n NMR STRUCTURE OF THE ALL-TRANS RETINAL IN DARK-ADAPTEDBACTERIORHODOPSIN
1r84 NMR STRUCTURE OF THE 13-CIS-15-SYN RETINAL IN DARK_ADAPTEDBACTERIORHODOPSIN
1s51 THR24SER BACTERIORHODOPSIN
1s52 THR24VAL BACTERIORHODOPSIN
1s53 THR46SER BACTERIORHODOPSIN
1s54 THR24ALA BACTERIORHODOPSIN
1tn0 STRUCTURE OF BACTERORHODOPSIN MUTANT A51P
1tn5 STRUCTURE OF BACTERORHODOPSIN MUTANT K41P
1ucq CRYSTAL STRUCTURE OF THE L INTERMEDIATE OF BACTERIORHODOPSIN
1vjm DEFORMATION OF HELIX C IN THE LOW- TEMPERATURE L-INTERMEDIATE OF BACTERIORHODOPSIN
1x0i CRYSTAL STRUCTURE OF THE ACID BLUE FORM OF BACTERIORHODOPSIN
1x0k CRYSTAL STRUCTURE OF BACTERIORHODOPSIN AT PH 10
1x0s CRYSTAL STRUCTURE OF THE 13-CIS ISOMER OF BACTERIORHODOPSIN
1xji BACTERIORHODOPSIN CRYSTALLIZED IN BICELLES AT ROOMTEMPERATURE
2at9 STRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM BY ELECTRON CRYSTALLOGRAPHY
2brd CRYSTAL STRUCTURE OF BACTERIORHODOPSIN IN PURPLE MEMBRANE
2wjl BACTERIORHODOPSIN MUTANT E194D