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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN STEAROYL ACYL CARRIER PROTEIN DESATURASE FROM RICINUS COMMUNIS (CASTOR BEAN) AND ACETATE.
 
Authors :  M. Moche, J. Shanklin, A. K. Ghoshal, Y. Lindqvist
Date :  07 Mar 03  (Deposition) - 13 May 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Di-Iron Enzyme, Four-Helix Bundle, Fatty Acid Biosynthesis, Electron Transfer, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Moche, J. Shanklin, A. Ghoshal, Y. Lindqvist
Azide And Acetate Complexes Plus Two Iron-Depleted Crystal Structures Of The Di-Iron Enzyme Delta9 Stearoyl-Acp Desaturase-Implications For Oxygen Activation And Catalytic Intermediates
J. Biol. Chem. V. 278 25072 2003
PubMed-ID: 12704186  |  Reference-DOI: 10.1074/JBC.M301662200

(-) Compounds

Molecule 1 - ACYL-[ACYL-CARRIER PROTEIN] DESATURASE
    Chains: A
    EC Number: 1.14.19.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET9D
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: CASTOR BEAN
    Organism Scientific: RICINUS COMMUNIS
    Organism Taxid: 3988
    Synonym: STEAROYL ACYL CARRIER PROTEIN DESATURASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2FE2Ligand/IonFE (III) ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2FE-1Ligand/IonFE (III) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:105 , GLU A:143 , HIS A:146 , GLU A:229 , ACT A:366BINDING SITE FOR RESIDUE FE A 364
2AC2SOFTWAREGLU A:143 , GLU A:196 , GLU A:229 , HIS A:232 , ACT A:366BINDING SITE FOR RESIDUE FE A 365
3AC3SOFTWAREGLU A:105 , GLU A:143 , GLU A:196 , THR A:199 , GLU A:229 , FE A:364 , FE A:365 , HOH A:443BINDING SITE FOR RESIDUE ACT A 366

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OQ9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OQ9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OQ9)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FATTY_ACID_DESATUR_2PS00574 Fatty acid desaturases family 2 signature.STAD_RICCO316-335  1A:283-302
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FATTY_ACID_DESATUR_2PS00574 Fatty acid desaturases family 2 signature.STAD_RICCO316-335  2A:283-302

(-) Exons   (0, 0)

(no "Exon" information available for 1OQ9)

(-) 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:338
 aligned with STAD_RICCO | P22337 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:346
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390      
           STAD_RICCO    51 FMPPREVHVQVTHSMPPQKIEIFKSLDNWAEENILVHLKPVEKCWQPQDFLPDPASDGFDEQVRELRERAKEIPDDYFVVLVGDMITEEALPTYQTMLNTLDGVRDETGASPTSWAIWTRAWTAEENRHGDLLNKYLYLSGRVDMRQIEKTIQYLIGSGMDPRTENSPYLGFIYTSFQERATFISHGNTARQAKEHGDIKLAQICGTIAADEKRHETAYTKIVEKLFEIDPDGTVLAFADMMRKKISMPAHLMYDGRDDNLFDHFSAVAQRLGVYTAKDYADILEFLVGRWKVDKLTGLSAEGQKAQDYVCRLPPRIRRLEERAQGRAKEAPTMPFSWIFDRQVKL 396
               SCOP domains d1oq9a_ A: delta 9-stearoyl-acyl carrier protein desaturase                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1oq9A00 A:18-363 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ---------------FA_desaturase_2-1oq9A01 A:33-361                                                                                                                                                                                                                                                                                                         -- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhh.....hhhhh.hhhhhh......hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhh...hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh.--------....eee.hhhh..eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FATTY_ACID_DESATUR_2------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oq9 A  18 FMPPREVHVQVTHSMPPQKIEIFKSLDNWAEENILVHLKPVEKCWQPQDFLPDPASDGFDEQVRELRERAKEIPDDYFVVLVGDMITEEALPTYQTMLNTLDGVRDETGASPTSWAIWTRAWTAEENRHGDLLNKYLYLSGRVDMRQIEKTIQYLIGSGMDPRTENSPYLGFIYTSFQERATFISHGNTARQAKEHGDIKLAQICGTIAADEKRHETAYTKIVEKLFEIDPDGTVLAFADMMRKKISMPAHLMYDGRDDNLFDHFSAVAQRLGVYTAKDYADILEFLVGRWKVDKLTGLSAEGQKAQDYVCRLPPRIRRL--------KEAPTMPFSWIFDRQVKL 363
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357      
                                                                                                                                                                                                                                                                                                                                                         337      346
   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  (1, 1)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Ferritin (185)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (STAD_RICCO | P22337)
molecular function
    GO:0045300    acyl-[acyl-carrier-protein] desaturase activity    Catalysis of the reaction: stearoyl-[acyl-carrier protein] + reduced acceptor + O2 = oleoyl-[acyl-carrier protein] + acceptor + H2O. The enzyme requires ferredoxin.
    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.
biological process
    GO:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    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.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

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  STAD_RICCO | P22337
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  1.14.19.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        STAD_RICCO | P22337: 1afr 1oq4 1oq7 1oqb 2j2f 2xz0 2xz1 4v0j

(-) Related Entries Specified in the PDB File

1afr THE CRYSTAL STRUCTURE OF STEAROYL ACYL CARRIER PROTEIN DESATURASE FROM RICINUS COMMUNIS (CASTOR BEAN).
1oq4 1OQ4 CONTAINS THE SAME PROTEIN COMPLEXED WITH FE AND AZI
1oq7 1OQ7 CONTAINS THE SAME PROTEIN COMPLEXED WITH STRONTIUM ION
1oqb 1OQB CONTAINS THE SAME PROTEIN COMPLEXED WITH FE