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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CYSTEINE DIOXYGENASE IN COMPLEX WITH SUBSTRATE CYSTEINE
 
Authors :  S. Ye, X. Wu, L. Wei, D. Tang, P. Sun, Z. Rao
Date :  12 Sep 06  (Deposition) - 05 Dec 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Cupin, Enzyme-Substrate Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Ye, X. Wu, L. Wei, D. Tang, P. Sun, M. Bartlam, Z. Rao
An Insight Into The Mechanism Of Human Cysteine Dioxygenase: Key Roles Of The Thioether-Bonded Tyrosine-Cysteine Cofactor.
J. Biol. Chem. V. 282 3391 2007
PubMed-ID: 17135237  |  Reference-DOI: 10.1074/JBC.M609337200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYSTEINE DIOXYGENASE TYPE 1
    ChainsA
    EC Number1.13.11.20
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX-6P-1
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneCDO1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCYSTEINE DIOXYGENASE TYPE I, CDO, CDO-I

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CYS2Mod. Amino AcidCYSTEINE
2FE21Ligand/IonFE (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:86 , HIS A:88 , HIS A:140 , CYS A:202BINDING SITE FOR RESIDUE FE2 A 201
2AC2SOFTWARETYR A:58 , ARG A:60 , HIS A:86 , HIS A:88 , HIS A:140 , HIS A:155 , TYR A:157 , FE2 A:201BINDING SITE FOR RESIDUE CYS A 202
3AC3SOFTWAREGLN A:34 , ARG A:123 , GLN A:129 , CYS A:130 , ALA A:131 , TYR A:132 , HOH A:381 , HOH A:399BINDING SITE FOR RESIDUE CYS A 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2IC1)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:158 -Pro A:159

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_023536T45ICDO1_HUMANPolymorphism1042867AT45I
2UniProtVAR_036170E143QCDO1_HUMANUnclassified  ---AE143Q
3CancerSNPVAR_CDO1_HUMAN_CCDS4121_1_01 *E143QCDO1_HUMANDisease (Colorectal cancer)  ---AE143Q
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2IC1)

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002505351aENSE00000972231chr5:115152651-115151925727CDO1_HUMAN1-57571A:6-5752
1.4cENST000002505354cENSE00000890256chr5:115148955-11514887878CDO1_HUMAN57-83271A:57-8327
1.5ENST000002505355ENSE00000972232chr5:115147012-115146858155CDO1_HUMAN83-135531A:83-13553
1.7ENST000002505357ENSE00000972233chr5:115142215-115142046170CDO1_HUMAN135-191571A:135-19056
1.8bENST000002505358bENSE00001005631chr5:115141159-115140430730CDO1_HUMAN192-20091A:202-2032

(-) 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:187
 aligned with CDO1_HUMAN | Q16878 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:188
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185        
           CDO1_HUMAN     6 VLKPRTLADLIRILHQLFAGDEVNVEEVQAIMEAYESDPTEWAMYAKFDQYRYTRNLVDQGNGKFNLMILCWGEGHGSSIHDHTNSHCFLKMLQGNLKETLFAWPDKKSNEMVKKSERVLRENQCAYINDSIGLHRVENISHTEPAVSLHLYSPPFDTCHAFDQRTGHKNKVTMTFHSKFGIRTPNAT 193
               SCOP domains d2ic1a1 A:6-190 Cysteine dioxygenase type I                                                                                                                                              --- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhh.......eeeeeehhhhh.eeeeeee.......ee.....eeeeeeee..eeeeee...........eeeeee.....eeee.....eeeeee......eeeeeeee....eeeee......eeeee....ee..ee..-.. Sec.struct. author
             SAPs(SNPs) (1) ---------------------------------------I-------------------------------------------------------------------------------------------------Q-------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------------------------------------------------------------------Q-------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:6-57 UniProt: 1-57 [INCOMPLETE]   -------------------------Exon 1.5  PDB: A:83-135 UniProt: 83-135              --------------------------------------------------------1. Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------Exon 1.4c  PDB: A:57-83    ---------------------------------------------------Exon 1.7  PDB: A:135-190 UniProt: 135-191 [INCOMPLETE]   -- Transcript 1 (2)
                 2ic1 A   6 VLKPRTLADLIRILHQLFAGDEVNVEEVQAIMEAYESDPTEWAMYAKFDQYRYTRNLVDQGNGKFNLMILCWGEGHGSSIHDHTNSHCFLKMLQGNLKETLFAWPDKKSNEMVKKSERVLRENQCAYINDSIGLHRVENISHTEPAVSLHLYSPPFDTCHAFDQRTGHKNKVTMTFHSKFGIRTP-CC 203
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185    | | 
                                                                                                                                                                                                                  190 | 
                                                                                                                                                                                                                    202 

   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/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2IC1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IC1)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CDO1_HUMAN | Q16878)
molecular function
    GO:0017172    cysteine dioxygenase activity    Catalysis of the reaction: L-cysteine + O(2) = 3-sulfino-L-alanine + H(+).
    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:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    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:0019448    L-cysteine catabolic process    The chemical reactions and pathways resulting in the breakdown of L-cysteine, the L-enantiomer of 2-amino-3-mercaptopropanoic acid, i.e. (2R)-2-amino-3-mercaptopropanoic acid.
    GO:0019451    L-cysteine catabolic process to pyruvate, using cysteine dioxygenase    The chemical reactions and pathways resulting in the breakdown into pyruvate of L-cystine, catalyzed by the enzyme cysteine dioxygenase (EC:1.13.11.20).
    GO:0006534    cysteine metabolic process    The chemical reactions and pathways involving cysteine, 2-amino-3-mercaptopropanoic acid.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0007595    lactation    The regulated release of milk from the mammary glands and the period of time that a mother lactates to feed her young.
    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.
    GO:0043200    response to amino acid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups.
    GO:0051591    response to cAMP    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
    GO:0045471    response to ethanol    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethanol stimulus.
    GO:0033762    response to glucagon    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucagon stimulus.
    GO:0051384    response to glucocorticoid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
    GO:0010243    response to organonitrogen compound    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.
    GO:0000097    sulfur amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids containing sulfur, comprising cysteine, methionine and selenocysteine.
    GO:0042412    taurine biosynthetic process    The chemical reactions and pathways resulting in the formation of taurine (2-aminoethanesulfonic acid), a sulphur-containing amino acid derivative important in the metabolism of fats.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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