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(-) Description

Title :  A PUTATIVE FE2+-BOUND PERSULFENATE INTERMEDIATE IN CYSTEINE DIOXYGENASE
 
Authors :  C. R. Simmons, M. H. Stipanuk, P. A. Karplus
Date :  22 Sep 08  (Deposition) - 21 Oct 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.42
Chains :  Asym./Biol. Unit :  A
Keywords :  Peroxysulfenate, Non-Heme Dioxygenases, Fe2+ Metalloenzyme, Cysteine, Taurine, Thioether, Dioxygenase, Iron, Metal- Binding, Oxidoreductase, Phosphoprotein, Thioether Bond (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. R. Simmons, K. Krishnamoorthy, S. L. Granett, D. J. Schuller, J. E. Dominy, T. P. Begley, M. H. Stipanuk, P. A. Karplus
A Putative Fe2+-Bound Persulfenate Intermediate In Cysteine Dioxygenase.
Biochemistry V. 47 11390 2008
PubMed-ID: 18847220  |  Reference-DOI: 10.1021/BI801546N
(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 StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePET32A
    GeneCDO1
    Organism CommonBROWN RAT,RAT,RATS
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymCYSTEINE DIOXYGENASE TYPE I, CDO-I, CDO

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
12CO1Ligand/IonS-HYDROPEROXYCYSTEINE
2FE21Ligand/IonFE (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:86 , HIS A:88 , HIS A:140 , 2CO A:580BINDING SITE FOR RESIDUE FE2 A 501
2AC2SOFTWARETYR A:58 , ARG A:60 , LEU A:75 , HIS A:86 , HIS A:88 , CYS A:93 , LEU A:95 , HIS A:140 , VAL A:142 , HIS A:155 , TYR A:157 , FE2 A:501BINDING SITE FOR RESIDUE 2CO A 580

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:4 -Glu A:5
2Ser A:158 -Pro A:159

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000001721ENSRNOE00000000927chr18:40928671-40928313359CDO1_RAT1-57571A:4-5754
1.2ENSRNOT000000001722ENSRNOE00000252649chr18:40924128-4092405178CDO1_RAT57-83271A:57-8327
1.3ENSRNOT000000001723ENSRNOE00000252644chr18:40921496-40921342155CDO1_RAT83-135531A:83-13553
1.4ENSRNOT000000001724ENSRNOE00000035450chr18:40916340-40916171170CDO1_RAT135-191571A:135-19056
1.5ENSRNOT000000001725ENSRNOE00000252662chr18:40914722-40914028695CDO1_RAT192-20090--

(-) 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_RAT | P21816 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:187
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       
             CDO1_RAT     4 TELLKPRTLADLIRILHELFAGDEVNVEEVQAVLEAYESNPAEWALYAKFDQYRYTRNLVDQGNGKFNLMILCWGEGHGSSIHDHTDSHCFLKLLQGNLKETLFDWPDKKSNEMIKKSERTLRENQCAYINDSIGLHRVENVSHTEPAVSLHLYSPPFDTCHAFDQRTGHKNKVTMTFHSKFGIRTP 190
               SCOP domains d3elna_ A: 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...........eeeeeee....eeee.....eeeee.......eeeeeeee....eeeee......eeeee....ee..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:4-57 UniProt: 1-57 [INCOMPLETE]      -------------------------Exon 1.3  PDB: A:83-135 UniProt: 83-135              ------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------Exon 1.2  PDB: A:57-83     ---------------------------------------------------Exon 1.4  PDB: A:135-190 UniProt: 135-191 [INCOMPLETE]   Transcript 1 (2)
                 3eln A   4 TELLKPRTLADLIRILHELFAGDEVNVEEVQAVLEAYESNPAEWALYAKFDQYRYTRNLVDQGNGKFNLMILCWGEGHGSSIHDHTDSHCFLKLLQGNLKETLFDWPDKKSNEMIKKSERTLRENQCAYINDSIGLHRVENVSHTEPAVSLHLYSPPFDTCHAFDQRTGHKNKVTMTFHSKFGIRTP 190
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       

   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 3ELN)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CDO1_RAT | P21816)
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:0046439    L-cysteine metabolic process    The chemical reactions and pathways involving L-cysteine, the L-enantiomer of 2-amino-3-mercaptopropanoic acid, i.e. (2R)-2-amino-3-mercaptopropanoic acid.
    GO:0006534    cysteine metabolic process    The chemical reactions and pathways involving cysteine, 2-amino-3-mercaptopropanoic acid.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        CDO1_RAT | P218162b5h 2gh2 4ieo 4iep 4ieq 4ier 4ies 4iet 4ieu 4iev 4iew 4iex 4iey 4iez 4jtn 4jto 4kwj 4kwk 4kwl 4pix 4piy 4piz 4pjy 4ubg 4ubh 4xet 4xez 4xf0 4xf1 4xf3 4xf4 4xf9 4xfa 4xfb 4xfc 4xff 4xfg 4xfh 4xfi 4yni 4ysf 4yyo 4z82 5efu 5ezw 5fdb 5i0r 5i0s 5i0t 5i0u

(-) Related Entries Specified in the PDB File

2b5h 2gh2