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(-) Description

Title :  STRUCTURE OF RPE65: P65 CRYSTAL FORM GROWN IN FOS-CHOLINE-10
 
Authors :  P. D. Kiser, K. Palczewski
Date :  09 May 12  (Deposition) - 03 Oct 12  (Release) - 02 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Monotopic Membrane Protein, Metalloprotein, Non-Heme Iron Protein, Beta-Propeller, Smooth Er Membrane, Isomerase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. D. Kiser, E. R. Farquhar, W. Shi, X. Sui, M. R. Chance, K. Palczewski
Structure Of Rpe65 Isomerase In A Lipidic Matrix Reveals Roles For Phospholipids And Iron In Catalysis.
Proc. Natl. Acad. Sci. Usa V. 109 E2747 2012
PubMed-ID: 23012475  |  Reference-DOI: 10.1073/PNAS.1212025109

(-) Compounds

Molecule 1 - RETINOID ISOMEROHYDROLASE
    Chains: A, B
    EC Number: 3.1.1.64
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: RPE65, RETINOID ISOMERASE, ALL-TRANS-RETINYL-PALMITATE HYDROLASE, RETINAL PIGMENT EPITHELIUM-SPECIFIC 65 KDA PROTEIN, RETINOL ISOMERASE
    Tissue: RETINA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1ETX3Ligand/Ion2-ETHOXYETHANOL
2FE22Ligand/IonFE (II) ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:180 , HIS A:241 , HIS A:313 , HIS A:527BINDING SITE FOR RESIDUE FE2 A 601
2AC2SOFTWARETYR A:137 , ALA A:177 , ASN A:191 , VAL A:207BINDING SITE FOR RESIDUE ETX A 602
3AC3SOFTWAREILE A:183 , GLU A:184 , ASN A:185 , LEU A:245 , TYR A:423 , GLY A:427BINDING SITE FOR RESIDUE ETX A 603
4AC4SOFTWAREHIS B:180 , HIS B:241 , HIS B:313 , HIS B:527BINDING SITE FOR RESIDUE FE2 B 601
5AC5SOFTWARETYR B:137 , VAL B:174 , GLY B:176 , ALA B:177 , ASN B:191 , VAL B:207BINDING SITE FOR RESIDUE ETX B 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F3D)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg A:124 -Gly A:125

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F3D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F3D)

(-) Exons   (0, 0)

(no "Exon" information available for 4F3D)

(-) 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:513
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhh........ee.eeee.......eeeeeeeeee.ee..ee.......eeeeeeeeee..eeeeeeee..hhhhhhhhhhh........................eeeee..eeeee....eeeee......eeeeee.hhh..........ee.....eeeeeee.......eeeeeee........hhhhhheeeeeee.............ee...eeeeee..eeehhhhhhhh...hhh.eee.....eeeeeee....eeeeeeeee..eeeeeeeeeeee..eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeee...hhhhh............eeee....eeeee.eeee....eeeeeee.hhhhhh.....eeeeeeee..eeeeeeeee.....eeee..........eeee.........eeeeeeee........eeeeeee.....eeeeeee.........eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f3d A   3 SQVEHPAGGYKKLFETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDGQALLHKFDFKEGHVTYHRRFIRTDAYVRAMTEKRIVITEFGTCAFPRGVEVTDNALVNIYPVGEDYYACTETNFITKVNPETLETIKQVDLCNYVSVNGATAHPHIENDGTVYNIGNCFGKNFSIAYNIVKIPPLQADKEDPISKSEIVVQFPCSDRFKPSYVHSFGLTPNYIVFVETPVKINLFKFLSSGANYMDCFESNETMGVWLHIADKKRKKYINNKYRTSPFNLFHHINTYEDHEFLIVDLCCWKGFEFVYNYLYLANLRENWEEVKKNARKAPQPEVRRYVLPLNIDKADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQINYQKYGGKPYTYAYGLGLNHFVPDRLCKLNVKTKETWVWQEPDSYPSEPIFVSHPDALEEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEVARAEVEINIPVTFHGLFKKS 533
                                    12        22        32        42        52        62        72        82        92       102      |126       136       146       156       166       176       186       196       206       216       226       236       246       256       266||     280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530   
                                                                                                                                    109|                                                                                                                                            267|                                                                                                                                                                                                                                                                     
                                                                                                                                     124                                                                                                                                             272                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:513
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhh........ee.eeee.......eeeeeeeeee.ee..ee.......eeeeeeeeee..eeeeeeee..hhhhhhhhhhh........................eeeee..eeeee....eeeee......eeeeee.hhh..........ee.....eeeeeee.......eeeeeee........hhhhhheeeeeee.............ee...eeeeee..eeehhhhhhhh...hhh.eee.....eeeeeee....eeeeeeeee..eeeeeeeeeeee..eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeee...hhhhh............eeee....eeeee.eeee....eeeeeee.hhhhhh.....eeeeeeee..eeeeeeeee.....eeee..........eeee.........eeeeeeee........eeeeeee.....eeeeeee.........eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f3d B   3 SQVEHPAGGYKKLFETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDGQALLHKFDFKEGHVTYHRRFIRTDAYVRAMTEKRIVITEFGTCAFPRGVEVTDNALVNIYPVGEDYYACTETNFITKVNPETLETIKQVDLCNYVSVNGATAHPHIENDGTVYNIGNCFGKNFSIAYNIVKIPPLQADKEDPISKSEIVVQFPCSDRFKPSYVHSFGLTPNYIVFVETPVKINLFKFLSSGANYMDCFESNETMGVWLHIADKKRKKYINNKYRTSPFNLFHHINTYEDHEFLIVDLCCWKGFEFVYNYLYLANLRENWEEVKKNARKAPQPEVRRYVLPLNIDKADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQINYQKYGGKPYTYAYGLGLNHFVPDRLCKLNVKTKETWVWQEPDSYPSEPIFVSHPDALEEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEVARAEVEINIPVTFHGLFKKS 533
                                    12        22        32        42        52        62        72        82        92       102      |126       136       146       156       166       176       186       196       206       216       226       236       246       256       266||     280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530   
                                                                                                                                    109|                                                                                                                                            267|                                                                                                                                                                                                                                                                     
                                                                                                                                     124                                                                                                                                             272
   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 4F3D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F3D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F3D)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:124 - Gly A:125   [ RasMol ]  
 

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  RPE65_BOVIN | Q28175
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  3.1.1.64
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

3fsn 4f2z 4f30 4f3a