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(-) Description

Title :  ENSEMBLE REFINEMENT OF THE PROTEIN CRYSTAL STRUCTURE OF CYSTEINE DIOXYGENASE TYPE I FROM MUS MUSCULUS MM.241056
 
Authors :  E. J. Levin, D. A. Kondrashov, G. E. Wesenberg, G. N. Phillips Jr. , Cent Eukaryotic Structural Genomics (Cesg)
Date :  31 May 07  (Deposition) - 19 Jun 07  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A  (16x)
Biol. Unit 1:  A  (1x)
Keywords :  Ensemble Refinement, Refinement Methodology Development, Mm. 241056, Pfam05995. 2 Cdo_i, Bc013638, Cupin Family, Structural Genomics, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. J. Levin, D. A. Kondrashov, G. E. Wesenberg, G. N. Phillips
Ensemble Refinement Of Protein Crystal Structures: Validation And Application.
Structure V. 15 1040 2007
PubMed-ID: 17850744  |  Reference-DOI: 10.1016/J.STR.2007.06.019
(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
    Expression System PlasmidPVP16
    Expression System StrainB834 P(RARE2)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneCDO1, MM.241056
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymCYSTEINE DIOXYGENASE TYPE I, CDO, CDO-I

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit (16x)A
Biological Unit 1 (1x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MSE3Mod. Amino AcidSELENOMETHIONINE
3NI1Ligand/IonNICKEL (II) ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MSE3Mod. Amino AcidSELENOMETHIONINE
3NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:86 , HIS A:88 , HIS A:140 , HOH A:359 , HOH A:360 , HOH A:361BINDING SITE FOR RESIDUE NI A 201
2AC2SOFTWAREASP A:162 , THR A:163BINDING SITE FOR RESIDUE EDO A 234

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q4S)

(-) Cis Peptide Bonds  (1, 16)

Asymmetric Unit
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16Ser A:158 -Pro A:159

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q4S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q4S)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q4S)

(-) 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:186
 aligned with CDO1_MOUSE | P60334 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:186
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184      
           CDO1_MOUSE     5 ELLKPRTLADLIRILHELFAGDEVNVEEVQAVLEAYESNPAEWALYAKFDQYRYTRNLVDQGNGKFNLMILCWGEGHGSSIHDHTDSHCFLKLLQGNLKETLFDWPDKKSNEMIKKSERTLRENQCAYINDSIGLHRVENVSHTEPAVSLHLYSPPFDTCHAFDQRTGHKNKVTMTFHSKFGIRTP 190
               SCOP domains d2q4sa_ A: Cysteine dioxygenase type I                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains CDO_I-2q4sA01 A:5-170                                                                                                                                                 -------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhh............eeeehhhhh.eeeeeee.......ee.....eeeeeeee..eeeeee.............eeeee....eeee.....eeeee.......eeeeeeee....eeeee......eeeee....ee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2q4s A   5 ELLKPRTLADLIRILHELFAGDEVNVEEVQAVLEAYESNPAEWALYAKFDQYRYTRNLVDQGNGKFNLmILCWGEGHGSSIHDHTDSHCFLKLLQGNLKETLFDWPDKKSNEmIKKSERTLRENQCAYINDSIGLHRVENVSHTEPAVSLHLYSPPFDTCHAFDQRTGHKNKVTmTFHSKFGIRTP 190
                                    14        24        34        44        54        64        74        84        94       104       114  |    124       134       144       154       164       174    |  184      
                                                                                               73-MSE                                     117-MSE                                                       179-MSE       

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Q4S)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)
Chain A   (CDO1_MOUSE | P60334)
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:0019452    L-cysteine catabolic process to taurine    The chemical reactions and pathways resulting in the breakdown of L-cysteine into other compounds, including taurine.
    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:0051149    positive regulation of muscle cell differentiation    Any process that activates or increases the frequency, rate or extent of muscle cell differentiation.
    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.
    GO:0019530    taurine metabolic process    The chemical reactions and pathways involving 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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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        CDO1_MOUSE | P603342atf

(-) Related Entries Specified in the PDB File

2atf ORIGINAL REFINEMENT BASED ON SAME DATA AND R-FREE SET.