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(-) Description

Title :  CRYSTAL STRUCTURE OF APOCAROTENOID OXYGENASE IN THE PRESENCE OF C8E6
 
Authors :  X. Sui, W. Shi, K. Palczewski, P. D. Kiser
Date :  15 Feb 14  (Deposition) - 19 Mar 14  (Release) - 21 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Monotopic Membrane Protein, Non-Heme Iron, Metalloenzyme, 4-His Iron Center, Beta Propeller, Carotenoid Oxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Sui, P. D. Kiser, T. Che, P. R. Carey, M. Golczak, W. Shi, J. Von Lintig, K. Palczewski
Analysis Of Carotenoid Isomerase Activity In A Prototypical Carotenoid Cleavage Enzyme, Apocarotenoid Oxygenase (Aco).
J. Biol. Chem. V. 289 12286 2014
PubMed-ID: 24648526  |  Reference-DOI: 10.1074/JBC.M114.552836

(-) Compounds

Molecule 1 - APOCAROTENOID-15,15'-OXYGENASE
    Chains: A, B, C, D
    EC Number: 1.13.11.75
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PET3A
    Gene: DIOX1, SLL1541
    Organism Scientific: SYNECHOCYSTIS SP.
    Organism Taxid: 1111708
    Strain: PCC 6803
    Synonym: ACO, 8'-APO-BETA-CAROTENAL 15,15'-OXYGENASE, DIOX1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2FE24Ligand/IonFE (II) ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FE21Ligand/IonFE (II) ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FE21Ligand/IonFE (II) ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FE21Ligand/IonFE (II) ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FE21Ligand/IonFE (II) ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:183 , HIS A:238 , HIS A:304 , HIS A:484 , HOH A:625BINDING SITE FOR RESIDUE FE2 A 501
2AC2SOFTWAREASN A:338 , ASN A:341 , ASP C:32BINDING SITE FOR RESIDUE CL A 502
3AC3SOFTWAREHIS B:183 , HIS B:238 , HIS B:304 , HIS B:484 , HOH B:606BINDING SITE FOR RESIDUE FE2 B 501
4AC4SOFTWAREASN B:132 , GLN B:153BINDING SITE FOR RESIDUE CL B 502
5AC5SOFTWAREASN B:338 , ASN B:341 , TRP D:31 , ASP D:32BINDING SITE FOR RESIDUE CL B 503
6AC6SOFTWAREHIS C:183 , HIS C:238 , HIS C:304 , HIS C:484 , HOH C:601BINDING SITE FOR RESIDUE FE2 C 501
7AC7SOFTWAREHIS D:183 , HIS D:238 , HIS D:304 , HIS D:484 , HOH D:605BINDING SITE FOR RESIDUE FE2 D 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OU8)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:419 -Pro A:420
2Ala B:419 -Pro B:420
3Ala C:419 -Pro C:420
4Ala D:419 -Pro D:420

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OU8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OU8)

(-) Exons   (0, 0)

(no "Exon" information available for 4OU8)

(-) 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:479
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh.......eeee...eee.......eeeeeeee...ee..ee..hhhhh.eeeeeeee......eeeeee..hhhhhhhhhhh.............hhhhhhh...........eeeee..eeeee......eee......eeee.................eee..hhhhh...eeeeeeeee..eeeeeeeee.....eeeeeeeeee........ee...eeeeee..eee.hhhhhh...hhhh.eee.....eeeeeee......eeeee...eeeeeeeeeee..eeeeeeeee..........hhhhhhhhhh...eeeeeeee....eeeeeeee...eeeee.hhhhh.....eeeeee...........eeeeee.....eeeee....ee....eeee.........eeeeeeeee....eeeeeeee.........eeee..........eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ou8 A  12 QRSYSPQDWLRGYQSQPQEWDYWVEDVEGSIPPDLQGTLYRNGPGLLEIGDRPLKHPFDGDGMVTAFKFPGDGRVHFQSKFVRTQGYVEEQKAGKMIYRGVFGSQPAGGWLKTIFDLRLKNIANTNITYWGDRLLALWEGGQPHRLEPSNLATIGLDDLGGILAEGQPLSAHPRIDPASTFDGGQPCYVTFSIKSSLSSTLTLLELDPQGKLLRQKTETFPGFAFIHDFAITPHYAIFLQNNVTLNGLPYLFGLRGAGECVQFHPDKPAQIILVPRDGGEIKRIPVQAGFVFHHANAFEENGKIILDSICYNSLPQVDTDGDFRSTNFDNLDPGQLWRFTIDPAAATVEKQLMVSRCCEFPVVHPQQVGRPYRYVYMGAAHHSTGNAPLQAILKVDLESGTETLRSFAPHGFAGEPIFVPRPGGVAEDDGWLLCLIYKADLHRSELVILDAQDITAPAIATLKLKHHIPYPLHGSWAQT 490
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481         


Chain B from PDB  Type:PROTEIN  Length:479
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh.......eeee...eee.......eeeeeeee...ee..ee..hhhhh.eeeeeeee......eeeeee..hhhhhhhhhhh.............hhhhhhh...........eeeee..eeeee......eee......eeee.................eee..hhhhh...eeeeeeeee..eeeeeeeee.....eeeeeeeeee........ee...eeeeee..eee.hhhhhh...hhhh.eee.....eeeeeee......eeeee...eeeeeeeeeee..eeeeeeeee..........hhhhhhhhhh...eeeeeeee....eeeeeeee...eeeee.hhhhh.....eeeeee...........eeeeee.....eeeee....ee....eeee.........eeeeeeeee....eeeeeeee.........eeee..........eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ou8 B  12 QRSYSPQDWLRGYQSQPQEWDYWVEDVEGSIPPDLQGTLYRNGPGLLEIGDRPLKHPFDGDGMVTAFKFPGDGRVHFQSKFVRTQGYVEEQKAGKMIYRGVFGSQPAGGWLKTIFDLRLKNIANTNITYWGDRLLALWEGGQPHRLEPSNLATIGLDDLGGILAEGQPLSAHPRIDPASTFDGGQPCYVTFSIKSSLSSTLTLLELDPQGKLLRQKTETFPGFAFIHDFAITPHYAIFLQNNVTLNGLPYLFGLRGAGECVQFHPDKPAQIILVPRDGGEIKRIPVQAGFVFHHANAFEENGKIILDSICYNSLPQVDTDGDFRSTNFDNLDPGQLWRFTIDPAAATVEKQLMVSRCCEFPVVHPQQVGRPYRYVYMGAAHHSTGNAPLQAILKVDLESGTETLRSFAPHGFAGEPIFVPRPGGVAEDDGWLLCLIYKADLHRSELVILDAQDITAPAIATLKLKHHIPYPLHGSWAQT 490
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481         


Chain C from PDB  Type:PROTEIN  Length:479
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh.......eeee...eee.......eeeeeeee...ee..ee..hhhhh.eeeeeeee......eeeeee..hhhhhhhhhhh.............hhhhhhh...........eeeee..eeeee......eee......eeee.................eee..hhhhh...eeeeeeeee..eeeeeeeee.....eeeeeeeeee........ee...eeeeee..eee.hhhhhh...hhhh.eee.....eeeeeee......eeeee...eeeeeeeeeee..eeeeeeeee..........hhhhhhhhhh...eeeeeeee....eeeeeeee...eeeee.hhhhh.....eeeeee...........eeeeee.....eeeee....ee....eeee.........eeeeeeeee....eeeeeeee.........eeee..........eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ou8 C  12 QRSYSPQDWLRGYQSQPQEWDYWVEDVEGSIPPDLQGTLYRNGPGLLEIGDRPLKHPFDGDGMVTAFKFPGDGRVHFQSKFVRTQGYVEEQKAGKMIYRGVFGSQPAGGWLKTIFDLRLKNIANTNITYWGDRLLALWEGGQPHRLEPSNLATIGLDDLGGILAEGQPLSAHPRIDPASTFDGGQPCYVTFSIKSSLSSTLTLLELDPQGKLLRQKTETFPGFAFIHDFAITPHYAIFLQNNVTLNGLPYLFGLRGAGECVQFHPDKPAQIILVPRDGGEIKRIPVQAGFVFHHANAFEENGKIILDSICYNSLPQVDTDGDFRSTNFDNLDPGQLWRFTIDPAAATVEKQLMVSRCCEFPVVHPQQVGRPYRYVYMGAAHHSTGNAPLQAILKVDLESGTETLRSFAPHGFAGEPIFVPRPGGVAEDDGWLLCLIYKADLHRSELVILDAQDITAPAIATLKLKHHIPYPLHGSWAQT 490
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481         


Chain D from PDB  Type:PROTEIN  Length:479
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh.......eeee...eee.......eeeeeeee...ee..ee..hhhhh.eeeeeeee......eeeeee..hhhhhhhhhhh.............hhhhhhh...........eeeee..eeeee......eee......eeee.................eee..hhhhh...eeeeeeeee..eeeeeeeee.....eeeeeeeeee........ee...eeeeee..eee.hhhhhh...hhhh.eee.....eeeeeee......eeeee...eeeeeeeeeee..eeeeeeeee..........hhhhhhhhhh...eeeeeeee....eeeeeeee...eeeee.hhhhh.....eeeeee...........eeeeee.....eeeee....ee....eeee.........eeeeeeeee....eeeeeeee.........eeee..........eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ou8 D  12 QRSYSPQDWLRGYQSQPQEWDYWVEDVEGSIPPDLQGTLYRNGPGLLEIGDRPLKHPFDGDGMVTAFKFPGDGRVHFQSKFVRTQGYVEEQKAGKMIYRGVFGSQPAGGWLKTIFDLRLKNIANTNITYWGDRLLALWEGGQPHRLEPSNLATIGLDDLGGILAEGQPLSAHPRIDPASTFDGGQPCYVTFSIKSSLSSTLTLLELDPQGKLLRQKTETFPGFAFIHDFAITPHYAIFLQNNVTLNGLPYLFGLRGAGECVQFHPDKPAQIILVPRDGGEIKRIPVQAGFVFHHANAFEENGKIILDSICYNSLPQVDTDGDFRSTNFDNLDPGQLWRFTIDPAAATVEKQLMVSRCCEFPVVHPQQVGRPYRYVYMGAAHHSTGNAPLQAILKVDLESGTETLRSFAPHGFAGEPIFVPRPGGVAEDDGWLLCLIYKADLHRSELVILDAQDITAPAIATLKLKHHIPYPLHGSWAQT 490
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481
   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 4OU8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OU8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OU8)

(-) Gene Ontology  (5, 5)

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  Cis Peptide Bonds
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    Ala D:419 - Pro D:420   [ RasMol ]  
 
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  4ou8
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  ACOX_SYNY3 | P74334
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  1.13.11.75
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 Related Entries

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

UniProtKB/Swiss-Prot
        ACOX_SYNY3 | P74334: 2biw 2bix 4ou9 5kja 5kjb 5kjd 5kk0

(-) Related Entries Specified in the PDB File

2biw 4ou9