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(-) Description

Title :  CRYSTAL STRUCTURE OF ORYZA SATIVA FATTY ACID ALPHA-DIOXYGENASE Y379F WITH PALMITIC ACID
 
Authors :  G. Zhu, M. Koszelak-Rosenblum, M. G. Malkowski
Date :  22 May 13  (Deposition) - 21 Aug 13  (Release) - 16 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym./Biol. Unit :  A
Keywords :  Piox, Cox-Like Protein, Fatty Acid Alpha-Dioxygenase, Heme Binding, Calcium Binding, Monotopic Membrane Protein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Zhu, M. Koszelak-Rosenblum, M. G. Malkowski
Crystal Structures Of Alpha-Dioxygenase From Oryza Sativa: Insights Into Substrate Binding And Activation By Hydrogen Peroxide.
Protein Sci. V. 22 1432 2013
PubMed-ID: 23934749  |  Reference-DOI: 10.1002/PRO.2327

(-) Compounds

Molecule 1 - FATTY ACID ALPHA-OXIDASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Common: RED RICE
    Organism Scientific: ORYZA SATIVA
    Organism Taxid: 4530

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 17)

Asymmetric/Biological Unit (9, 17)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2BOG2Ligand/IonB-OCTYLGLUCOSIDE
3CA1Ligand/IonCALCIUM ION
4CL2Ligand/IonCHLORIDE ION
5HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
6IMD1Ligand/IonIMIDAZOLE
7PG41Ligand/IonTETRAETHYLENE GLYCOL
8PGE6Ligand/IonTRIETHYLENE GLYCOL
9PLM2Ligand/IonPALMITIC ACID

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:149 , GLN A:153 , VAL A:156 , ASP A:161 , HIS A:162 , ASN A:260 , TRP A:262 , THR A:376 , PHE A:379 , MET A:381 , HIS A:382 , PHE A:453 , LEU A:472 , LEU A:475 , ARG A:479 , ARG A:483 , IMD A:705 , HOH A:829 , HOH A:860 , HOH A:981 , HOH A:1280BINDING SITE FOR RESIDUE HEM A 701
02AC2SOFTWAREARG A:57 , HIS A:311 , ALA A:331 , PHE A:379 , PHE A:552 , ALA A:556 , ARG A:559 , HOH A:808BINDING SITE FOR RESIDUE PLM A 702
03AC3SOFTWAREASP A:158 , THR A:210 , TRP A:212 , ASP A:214 , SER A:216BINDING SITE FOR RESIDUE CA A 703
04AC4SOFTWAREGLY A:350 , PRO A:351 , ILE A:352 , LEU A:353BINDING SITE FOR RESIDUE PLM A 704
05AC5SOFTWAREGLN A:153 , VAL A:156 , HIS A:157 , ARG A:259 , ASN A:260 , HEM A:701BINDING SITE FOR RESIDUE IMD A 705
06AC6SOFTWAREPHE A:24 , GLY A:28 , PHE A:31 , LEU A:51 , ASN A:54 , THR A:55 , BOG A:710 , PGE A:713 , HOH A:958 , HOH A:1084BINDING SITE FOR RESIDUE BOG A 706
07AC7SOFTWAREASN A:39 , HIS A:42 , ARG A:492 , ILE A:498 , PRO A:499 , ILE A:500 , ASP A:505 , LYS A:537 , LYS A:538 , GLU A:546 , HOH A:830 , HOH A:1026 , HOH A:1162 , HOH A:1171 , HOH A:1238 , HOH A:1275BINDING SITE FOR RESIDUE 1PE A 707
08AC8SOFTWARETYR A:63 , GLU A:490 , ARG A:493 , ARG A:494BINDING SITE FOR RESIDUE PGE A 708
09AC9SOFTWARELYS A:606 , SER A:608 , TYR A:618 , HOH A:1096BINDING SITE FOR RESIDUE PGE A 709
10BC1SOFTWAREASN A:54 , ARG A:57 , PRO A:351 , ILE A:352 , BOG A:706 , HOH A:964 , HOH A:1206BINDING SITE FOR RESIDUE BOG A 710
11BC2SOFTWAREALA A:67 , VAL A:68 , ARG A:70 , SER A:72 , ASN A:96 , GLU A:98 , PHE A:105 , HOH A:944 , HOH A:957 , HOH A:1028BINDING SITE FOR RESIDUE PG4 A 711
12BC3SOFTWAREGLY A:240 , ASP A:241 , GLY A:243 , LYS A:274 , ARG A:469 , HOH A:851BINDING SITE FOR RESIDUE PGE A 712
13BC4SOFTWAREPHE A:24 , ALA A:34 , ARG A:38 , BOG A:706BINDING SITE FOR RESIDUE PGE A 713
14BC5SOFTWAREPHE A:24 , LYS A:62 , GLY A:349 , PGE A:715BINDING SITE FOR RESIDUE PGE A 714
15BC6SOFTWAREGLY A:350 , PGE A:714BINDING SITE FOR RESIDUE PGE A 715
16BC7SOFTWARELYS A:309 , TRP A:333 , HOH A:1003BINDING SITE FOR RESIDUE CL A 716
17BC8SOFTWAREARG A:330 , GLY A:338 , LYS A:339 , HOH A:898BINDING SITE FOR RESIDUE CL A 717

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:121 -Pro A:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KVL)

(-) 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:610
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhh.....................ee.................hhhhhhhhhh............hhhhhhhhhhhhhhhh........eeee.hhhhhh.....eeee.....ee.......ee.ee.......hhhhhh.hhhhhhhhh...............................hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhh.........................hhhhhhhhhhhhhh..eeeee.............eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhh..............hhhhhhhhhhhhh...hhhhhhhhh......hhhhh..hhhhhhhhhhhhh......hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kvl A   9 SVHPDLRDVFSKMSFFDKIGFLFIHAFDKRNLWHKVPVPIGLLYLNTRRTLLEKYNLLAVGRSSHGALFDPKEFLYRTEDGKYNDPHNAEAGSQNTFFGRNMEPVDQQDELMSPDPFVVATKLLARREYKDTGKQFNILAAAWIQFMVHDWMDHMEDTGQIGITAPKEVANECPLKSFKFHPTKELPTNSDGIKIGHYNIRTAWWDGSAVYGNNEERAEKLRTYVDGKLVIGDDGLLLHKENGVALSGDIRNSWAGVSILQALFVKEHNAVCDAIKEEHPNLSDEELYRYAKLVTSAVIAKVHTIDWTVELLKTKTMRAAMRANWYGLLGKKIKDTFGHIGGPILGGLVGLKKPNNHGVPYSLTEEFTSVFRMHSLIPSTLKLRDPTGQPDANNSPPCLEDIDIGEMIGLKGEEQLSKIGFEKQALSMGYQACGALELWNYPSFFRNLIPQNLDGTNRSDRIDLAALEVYRDRERSVPRYNEFRRRLFLIPIKSWEDLTSDKDAIETIRAIYGDDVEKLDLLVGLMAEKKIKGFAISETAFNIFILMASRRLEADRFFTSNFNEETYTKKGMQWVKTTEGLRDVINRHYPEITAKWMKSSSAFSVWDADY 618
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618
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  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 4KVL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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        Q9M5J1_ORYSA | Q9M5J1: 4kvj 4kvk

(-) Related Entries Specified in the PDB File

4kvj 4kvk