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(-) Description

Title :  CRYSTAL STRUCTURE OF BOVINE RPE65 AT 1.9 ANGSTROM RESOLUTION
 
Authors :  P. D. Kiser, D. T. Lodowski, M. Golczak, K. Palczewski
Date :  29 Nov 09  (Deposition) - 02 Feb 10  (Release) - 12 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  7-Bladed Beta-Propeller, Monotopic Membrane Protein, Sensory Transduction, Vision, Isomerase, Non-Heme Iron Protein, Acetylation, Cell Membrane, Cytoplasm, Hydrolase, Iron, Lipoprotein, Membrane, Metal-Binding, Palmitate, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Golczak, P. D. Kiser, D. T. Lodowski, A. Maeda, K. Palczewski
Importance Of Membrane Structural Integrity For Rpe65 Retinoid Isomerization Activity.
J. Biol. Chem. V. 285 9667 2010
PubMed-ID: 20100834  |  Reference-DOI: 10.1074/JBC.M109.063941

(-) Compounds

Molecule 1 - RETINOID ISOMEROHYDROLASE
    Chains: A, B
    EC Number: 3.1.1.64, 5.2.1.7
    Organism Common: BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Other Details: RETINAL PIGMENT EPITHELIUM MICROSOMES
    Synonym: ALL-TRANS-RETINYL-PALMITATE HYDROLASE, RETINOL ISOMERASE, RETINAL PIGMENT EPITHELIUM-SPECIFIC 65 KDA PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1FE22Ligand/IonFE (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:180 , HIS A:241 , HIS A:313 , HIS A:527BINDING SITE FOR RESIDUE FE2 A 534
2AC2SOFTWAREHIS B:180 , HIS B:241 , HIS B:313 , HIS B:527BINDING SITE FOR RESIDUE FE2 B 534

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KVC)

(-) 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:498
 aligned with RPE65_BOVIN | Q28175 from UniProtKB/Swiss-Prot  Length:533

    Alignment length:531
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532 
          RPE65_BOVIN     3 SQVEHPAGGYKKLFETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDGQALLHKFDFKEGHVTYHRRFIRTDAYVRAMTEKRIVITEFGTCAFPDPCKNIFSRFFSYFRGVEVTDNALVNIYPVGEDYYACTETNFITKVNPETLETIKQVDLCNYVSVNGATAHPHIENDGTVYNIGNCFGKNFSIAYNIVKIPPLQADKEDPISKSEIVVQFPCSDRFKPSYVHSFGLTPNYIVFVETPVKINLFKFLSSWSLWGANYMDCFESNETMGVWLHIADKKRKKYINNKYRTSPFNLFHHINTYEDHEFLIVDLCCWKGFEFVYNYSYLANLRENWEEVKKNARKAPQPEVRRYVLPLNIDKADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQINYQKYGGKPYTYAYGLGLNHFVPDRLCKLNVKTKETWVWQEPDSYPSEPIFVSHPDALEEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEVARAEVEINIPVTFHGLFKKS 533
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhh........ee.eeee.......eeeeeeee...ee..ee........eeeeeeeee..eeeeeeee..hhhhhhhhhhh...........-------------------........eeeee..eeeee....eeeee......eeeeeehhhhh.........ee.....eeeeeee..---..eeeeeee........hhhhhheeeeeee.............ee...eeeeee..eee.-----------...hhh.eee.....eeeeeee....eeeeeeeee..eeeeeeeeeeee..eeeeeeeeee...hhhhhhhhhhhh.hhhhhhhhhh...eeeeeeeeee...hhhhh............eeee....eeeee.eeee....eeeeeee.hhhhhh.....eeeeeeee..eeeeeeeee.....eeee..........eeee.........eeeeeeee........eeeeeee.....eeeeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kvc A   3 SQVEHPAGGYKKLFETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDGQALLHKFDFKEGHVTYHRRFIRTDAYVRAMTEKRIVITEFGTCA-------------------EVTDNALVNIYPVGEDYYACTETNFITKVNPETLETIKQVDLCNYVSVNGATAHPHIENDGTVYNIGNCFG---SIAYNIVKIPPLQADKEDPISKSEIVVQFPCSDRFKPSYVHSFGLTPNYIVFVETPVKIN-----------GANYMDCFESNETMGVWLHIADKKRKKYINNKYRTSPFNLFHHINTYEDHEFLIVDLCCWKGFEFVYNYLYLANLRENWEEVKKNARKAPQPEVRRYVLPLNIDKADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQINYQKYGGKPYTYAYGLGLNHFVPDRLCKLNVKTKETWVWQEPDSYPSEPIFVSHPDALEEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEVARAEVEINIPVTFHGLFKKS 533
                                    12        22        32        42        52        62        72        82        92       102    |    -         -    |  132       142       152       162       172       182       192    |  202       212       222       232       242       252       | -       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532 
                                                                                                                                  107                 127                                                                   197 201                                                        260         272                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:497
 aligned with RPE65_BOVIN | Q28175 from UniProtKB/Swiss-Prot  Length:533

    Alignment length:531
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532 
          RPE65_BOVIN     3 SQVEHPAGGYKKLFETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDGQALLHKFDFKEGHVTYHRRFIRTDAYVRAMTEKRIVITEFGTCAFPDPCKNIFSRFFSYFRGVEVTDNALVNIYPVGEDYYACTETNFITKVNPETLETIKQVDLCNYVSVNGATAHPHIENDGTVYNIGNCFGKNFSIAYNIVKIPPLQADKEDPISKSEIVVQFPCSDRFKPSYVHSFGLTPNYIVFVETPVKINLFKFLSSWSLWGANYMDCFESNETMGVWLHIADKKRKKYINNKYRTSPFNLFHHINTYEDHEFLIVDLCCWKGFEFVYNYSYLANLRENWEEVKKNARKAPQPEVRRYVLPLNIDKADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQINYQKYGGKPYTYAYGLGLNHFVPDRLCKLNVKTKETWVWQEPDSYPSEPIFVSHPDALEEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEVARAEVEINIPVTFHGLFKKS 533
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------RPE65-3kvcB01 B:13-533                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Pfam domains (1)
           Pfam domains (2) ----------RPE65-3kvcB02 B:13-533                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Pfam domains (2)
         Sec.struct. author .......hhhhhhhh........ee.eeee.......eeeeeeeeee.ee..ee.......eeeeeeeeee..eeeeeeee..hhhhhhhhhhh...........-------------------........eeeee..eeeee....eeeee......eeeeee.hhh..........ee.....eeeeeee..---..eeeeeee........hhhhhheeeeeee.............ee...eeeeee..eee.------------..hhh.eee.....eeeeeee....eeeeeeeee..eeeeeeeeeeee..eeeeeeeeee...hhhhhhhhhhhh.hhhhhhhhh....eeeeeeeeee...hhhhh............eeee....eeeee.eeee....eeeeeee.hhhhhh.....eeeeeeee..eeeeeeeee.....eeee.....ee...eeee.........eeeeeeee........eeeeeee.....eeeeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kvc B   3 SQVEHPAGGYKKLFETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDGQALLHKFDFKEGHVTYHRRFIRTDAYVRAMTEKRIVITEFGTCA-------------------EVTDNALVNIYPVGEDYYACTETNFITKVNPETLETIKQVDLCNYVSVNGATAHPHIENDGTVYNIGNCFG---SIAYNIVKIPPLQADKEDPISKSEIVVQFPCSDRFKPSYVHSFGLTPNYIVFVETPVKIN------------ANYMDCFESNETMGVWLHIADKKRKKYINNKYRTSPFNLFHHINTYEDHEFLIVDLCCWKGFEFVYNYLYLANLRENWEEVKKNARKAPQPEVRRYVLPLNIDKADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQINYQKYGGKPYTYAYGLGLNHFVPDRLCKLNVKTKETWVWQEPDSYPSEPIFVSHPDALEEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEVARAEVEINIPVTFHGLFKKS 533
                                    12        22        32        42        52        62        72        82        92       102    |    -         -    |  132       142       152       162       172       182       192    |  202       212       222       232       242       252       | -         -|      282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532 
                                                                                                                                  107                 127                                                                   197 201                                                        260          273
   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 3KVC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: RPE65] (2)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RPE65_BOVIN | Q28175)
molecular function
    GO:0052885    all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity    Catalysis of the reaction: H(2)O + all-trans-retinyl ester = 11-cis-retinol + fatty acid.
    GO:0052884    all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity    Catalysis of the reaction: H(2)O + all-trans-retinyl palmitate = 11-cis-retinol + H(+) + palmitate.
    GO:1901612    cardiolipin binding    Interacting selectively and non-covalently with cardiolipin.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016702    oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from one donor, and two oxygen atoms is incorporated into a donor.
    GO:0031210    phosphatidylcholine binding    Interacting selectively and non-covalently with phosphatidylcholine, a class of glycophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of choline.
    GO:0001786    phosphatidylserine binding    Interacting selectively and non-covalently with phosphatidylserine, a class of glycophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of L-serine.
    GO:0004744    retinal isomerase activity    Catalysis of the reaction: all-trans-retinal = 11-cis-retinal.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    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:0042572    retinol metabolic process    The chemical reactions and pathways involving retinol, one of the three compounds that makes up vitamin A.
    GO:0007601    visual perception    The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031090    organelle membrane    A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.
    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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  3kvc
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  RPE65_BOVIN | Q28175
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 Related Entries

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

UniProtKB/Swiss-Prot
        RPE65_BOVIN | Q28175: 3fsn 4f2z 4f30 4f3a 4f3d 4rsc 4rse 4ryx 4ryy 4ryz 4zhk 5ul5 5ulg

(-) Related Entries Specified in the PDB File

3fsn