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(-) Description

Title :  STRUCTURE OF A CALCIUM-DEPENDENT 11R-LIPOXYGENASE SUGGESTS A MECHANISM FOR CA-REGULATION
 
Authors :  P. Eek, R. Jarving, I. Jarving, N. C. Gilbert, M. E. Newcomer, N. Samel
Date :  09 Jan 12  (Deposition) - 16 May 12  (Release) - 25 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.47
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Lox, Plat, Beta Sandwich, C2-Like Domain, Non-Heme Iron, Conformational Change, Dioxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Eek, R. Jarving, I. Jarving, N. C. Gilbert, M. E. Newcomer, N. Samel
Structure Of A Calcium-Dependent 11R-Lipoxygenase Suggests Mechanism For Ca2+ Regulation.
J. Biol. Chem. V. 287 22377 2012
PubMed-ID: 22573333  |  Reference-DOI: 10.1074/JBC.M112.343285

(-) Compounds

Molecule 1 - 11R-LIPOXYGENASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: GERSEMIA FRUTICOSA
    Organism Taxid: 134440

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1FE22Ligand/IonFE (II) ION
2SUC2Ligand/IonSUCROSE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1FE21Ligand/IonFE (II) ION
2SUC1Ligand/IonSUCROSE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1FE21Ligand/IonFE (II) ION
2SUC1Ligand/IonSUCROSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:373 , HIS A:378 , HIS A:556 , ASN A:560 , ILE A:679 , HOH A:942BINDING SITE FOR RESIDUE FE2 A 701
2AC2SOFTWAREASP A:466 , GLY A:467 , ARG A:469 , LYS A:474 , ASP A:475 , LEU A:478 , HOH A:848 , HOH A:931 , HOH A:935BINDING SITE FOR RESIDUE SUC A 702
3AC3SOFTWAREHIS B:373 , HIS B:378 , HIS B:556 , ASN B:560 , ILE B:679BINDING SITE FOR RESIDUE FE2 B 701
4AC4SOFTWAREARG B:461 , ASP B:466 , GLY B:467 , LEU B:468 , LYS B:474 , ASP B:475 , LEU B:478 , HOH B:830 , HOH B:839 , HOH B:952 , HOH B:998BINDING SITE FOR RESIDUE SUC B 702

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VF1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VF1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VF1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VF1)

(-) Exons   (0, 0)

(no "Exon" information available for 3VF1)

(-) 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:680
 aligned with Q2N410_9CNID | Q2N410 from UniProtKB/TrEMBL  Length:679

    Alignment length:680
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679
         Q2N410_9CNID     - -MKYKITVETGDLRGAGTDASVSIKLTGKDGAETSAFSLDKDFHNDFESGGTDTYDQSGVDVGEIAMITLKENGFGLKSDWYIAKVIIEKIDEATGFSNKYIFPCYRWVIKQLVVYEGKAILPNSKDNVKTIAEQRTKEVSENKKLYKWGTDPRYVQDLPGFVDAEEPKSLPKDVQFTDEATSSLFRVGLADFANLGLSHLFGIWDDWDCLEDFRQLITPAIKSGLPHAAEYWRDDVWFGSQFLNGSNPEVIRRCDKLPENFPVKNEMVEKLLDRGYTLEKAMKEGLIFITDYKILEGIPTMDTPEDKRYITTPLGLFYLKNNDDIIPIAIQLYQQPGENNSIWTPLKDTEWDWIMAKLWLRCADTQYHQMITHLLRCHLMMEPTAVSSWRNLPSVHPVWKLLYPHTKGIMAINTLGRNDLIPTGGAADKVLSIGGGGQVTLMQKHYRSVTFDSYDLVKDLRQRGVDGLRKFYYKDDALLLWNVIHQFVQDIIQIYYNDDDSVKKDNEIQDWIRDLHENGYPAGSDGTDKKVPKSFENREELVHFLTVVVFTCSCQHAAVNFSQMATYGFHPNSPTLMRQPPPTEKGKSNHKVIMASLANKHQAVTMVSVVNALTTIYPTEKFLGDYADNLFGDAAAHAAMAKFKSNLANITKQITERNQGMVSPYTWLIPGHVPNSIAI 679
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee...........eeeeeee........eee............eeeeeeee.....eeeeeeee.........eeeeeeeeee......eeeeeeeeeee...eeeee............hhhhhhhhhhhhhhhhhhh....hhhhh..........hhhhhhhhhh..hhhhhhh...hhhhhhhhhhhhhh.......hhhhhhhhh.........hhhhhh.hhhhhhhhhhhh......ee..........hhhhhhhhh....hhhhhhhh..eeeee.hhhh.....ee..ee......eeeeee.....eeeeeee..........ee.....hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhh.hhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vf1 A   0 HMKYKITVETGDLRGAGTDASVSIKLTGKDGAETSAFSLDKYFHNDFESGGTDTYDQSGVDVGEIAMITLKENGFGLKSDWYIAKVIIEKIDEATGFSNKYIFPCYRWVIKQLVVYEGKAILPNSKDNVKTIAEQRTKEVSENKKLYKWGTDPRYVQDLPGFVDAEEPKSLPKDVQFTDEATSSLFRVGLADFANLGLSHLFGIWDDWDCLEDFRQLITPAIKSGLPHAAEYWRDDVWFGSQFLNGSNPEVIRRCDKLPENFPVKNEMVEKLLDRGYTLEKAMKEGLIFITDYKILEGIPTMDTPEDKRYITTPLGLFYLKNNDDIIPIAIQLYQQPGENNSIWTPLKDTEWDWIMAKLWLRCADTQYHQMITHLLRCHLMMEPTAVSSWRNLPSVHPVWKLLYPHTKGIMAINTLGRNDLIPTGGAADKVLSIGGGGQVTLMQKHYRSVTFDSYDLVKDLRQRGVDGLRKFYYKDDALLLWNVIHQFVQDIIQIYYNDDDSVKKDNEIQDWIRDLHENGYPAGSDGTDKKVPKSFENREELVHFLTVVVFTCSCQHAAVNFSQMATYGFHPNSPTLMRQPPPTEKGKSNHKVIMASLANKHQAVTMVSVVNALTTIYPTEKFLGDYADNLFGDAAAHAAMAKFKSNLANITKQITERNQGMVSPYTWLIPGHVPNSIAI 679
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679


Chain B from PDB  Type:PROTEIN  Length:680
 aligned with Q2N410_9CNID | Q2N410 from UniProtKB/TrEMBL  Length:679

    Alignment length:680
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679
         Q2N410_9CNID     - -MKYKITVETGDLRGAGTDASVSIKLTGKDGAETSAFSLDKDFHNDFESGGTDTYDQSGVDVGEIAMITLKENGFGLKSDWYIAKVIIEKIDEATGFSNKYIFPCYRWVIKQLVVYEGKAILPNSKDNVKTIAEQRTKEVSENKKLYKWGTDPRYVQDLPGFVDAEEPKSLPKDVQFTDEATSSLFRVGLADFANLGLSHLFGIWDDWDCLEDFRQLITPAIKSGLPHAAEYWRDDVWFGSQFLNGSNPEVIRRCDKLPENFPVKNEMVEKLLDRGYTLEKAMKEGLIFITDYKILEGIPTMDTPEDKRYITTPLGLFYLKNNDDIIPIAIQLYQQPGENNSIWTPLKDTEWDWIMAKLWLRCADTQYHQMITHLLRCHLMMEPTAVSSWRNLPSVHPVWKLLYPHTKGIMAINTLGRNDLIPTGGAADKVLSIGGGGQVTLMQKHYRSVTFDSYDLVKDLRQRGVDGLRKFYYKDDALLLWNVIHQFVQDIIQIYYNDDDSVKKDNEIQDWIRDLHENGYPAGSDGTDKKVPKSFENREELVHFLTVVVFTCSCQHAAVNFSQMATYGFHPNSPTLMRQPPPTEKGKSNHKVIMASLANKHQAVTMVSVVNALTTIYPTEKFLGDYADNLFGDAAAHAAMAKFKSNLANITKQITERNQGMVSPYTWLIPGHVPNSIAI 679
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee...........eeeeeee........eee............eeeeeeee.....eeeeeeee.........eeeeeeeeee......eeeeeeeeeee...eeeee............hhhhhhhhhhhhhhhhhhh....hhhhh..........hhhhhhhhhh..hhhhhhh...hhhhhhhhhhhhhh.......hhhhhhhhh.........hhhhhh.hhhhhhhhhhhh......ee..........hhhhhhhhh....hhhhhhhh..eeeee.hhhh.....ee..ee......eeeeee.....eeeeeee..........ee.....hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhh.hhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vf1 B   0 HMKYKITVETGDLRGAGTDASVSIKLTGKDGAETSAFSLDKYFHNDFESGGTDTYDQSGVDVGEIAMITLKENGFGLKSDWYIAKVIIEKIDEATGFSNKYIFPCYRWVIKQLVVYEGKAILPNSKDNVKTIAEQRTKEVSENKKLYKWGTDPRYVQDLPGFVDAEEPKSLPKDVQFTDEATSSLFRVGLADFANLGLSHLFGIWDDWDCLEDFRQLITPAIKSGLPHAAEYWRDDVWFGSQFLNGSNPEVIRRCDKLPENFPVKNEMVEKLLDRGYTLEKAMKEGLIFITDYKILEGIPTMDTPEDKRYITTPLGLFYLKNNDDIIPIAIQLYQQPGENNSIWTPLKDTEWDWIMAKLWLRCADTQYHQMITHLLRCHLMMEPTAVSSWRNLPSVHPVWKLLYPHTKGIMAINTLGRNDLIPTGGAADKVLSIGGGGQVTLMQKHYRSVTFDSYDLVKDLRQRGVDGLRKFYYKDDALLLWNVIHQFVQDIIQIYYNDDDSVKKDNEIQDWIRDLHENGYPAGSDGTDKKVPKSFENREELVHFLTVVVFTCSCQHAAVNFSQMATYGFHPNSPTLMRQPPPTEKGKSNHKVIMASLANKHQAVTMVSVVNALTTIYPTEKFLGDYADNLFGDAAAHAAMAKFKSNLANITKQITERNQGMVSPYTWLIPGHVPNSIAI 679
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679
   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 3VF1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VF1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VF1)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q2N410_9CNID | Q2N410)
molecular function
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    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.
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.

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  3vf1
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