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(-) Description

Title :  CRYSTAL STRUCTURE OF MUS MUSCULUS IODOTYROSINE DEIODINASE (IYD) C217A, C239A BOUND TO FMN
 
Authors :  J. M. Buss, P. M. Mctamney, S. E. Rokita
Date :  02 Sep 11  (Deposition) - 29 Feb 12  (Release) - 04 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Flavoprotein, Membrane, Transmembrane, Dehalogenase, Iodide Salvage, Mono-Iodotyrosine, Nadp (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Buss, P. M. Mctamney, S. E. Rokita
Expression Of A Soluble Form Of Iodotyrosine Deiodinase For Active Site Characterization By Engineering The Native Membrane Protein From Mus Musculus.
Protein Sci. V. 21 351 2012
PubMed-ID: 22238141  |  Reference-DOI: 10.1002/PRO.2020

(-) Compounds

Molecule 1 - IODOTYROSINE DEIODINASE 1
    Chains: A, B
    EC Number: 1.22.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32A
    Expression System Strain: ROSETTA2(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: IYD-1
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: 10090
    Synonym: IYD-1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:7 , HOH A:20 , ARG A:96 , ARG A:97 , SER A:98 , ARG A:100 , VAL A:232 , THR A:233 , THR A:234 , THR A:235 , ARG A:275 , PRO B:123 , SER B:124 , GLY B:125 , SER B:212 , ACT B:302BINDING SITE FOR RESIDUE FMN A 301
2AC2SOFTWAREHOH A:17 , SER A:103 , SER A:104 , ARG A:266 , THR B:284 , VAL B:285 , HIS B:286BINDING SITE FOR RESIDUE PO4 A 303
3AC3SOFTWAREGLY A:125 , ALA A:126 , FMN B:301BINDING SITE FOR RESIDUE ACT A 302
4AC4SOFTWAREFMN A:301 , ALA B:126BINDING SITE FOR RESIDUE ACT B 302
5AC5SOFTWAREPRO A:123 , SER A:124 , GLY A:125 , SER A:212 , ACT A:302 , ARG B:96 , ARG B:97 , SER B:98 , ARG B:100 , VAL B:232 , THR B:233 , THR B:234 , THR B:235 , ARG B:275BINDING SITE FOR RESIDUE FMN B 301
6AC6SOFTWARETHR A:284 , VAL A:285 , HIS A:286 , HOH B:14 , SER B:103 , SER B:104 , ARG B:266BINDING SITE FOR RESIDUE PO4 B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TO0)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:153 -Glu A:154
2Glu B:153 -Glu B:154

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TO0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TO0)

(-) Exons   (0, 0)

(no "Exon" information available for 3TO0)

(-) 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:184
 aligned with IYD1_MOUSE | Q9DCX8 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:219
                                                                                                                                                                                                                                                   285 
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       | 
           IYD1_MOUSE    68 EHIPFSHTRYPEQEMRMRSQEFYELLNKRRSVRFISSEHVPMEVIENVIKAAGTAPSGAHTEPWTFVVVKDPDMKHKIREIIEEEEEINYMKRMGKRWVTDLKKLRTNWIKEYLDTAPVLILIFKQVHGFAANGKKKVHYYNEISVSIACGLLLAALQNAGLVTVTTTPLNCGPRLRVLLGRPSHEKLLVLLPVGYPSRDATVPDLKRKALDQIMVTV-   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee......hhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhh...hhhhh..eeeeee.hhhhhhhhhhhhhhh...----------------------.hhhhhh.eeeeeeee.-------------.hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh....eeeeeeeee.......eee.....hhhh.eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3to0 A  68 EHIPFSHTRYPEQEMRMRSQEFYELLNKRRSVRFISSEHVPMEVIENVIKAAGTAPSGAHTEPWTFVVVKDPDMKHKIREIIEEEEEI----------------------KEYLDTAPVLILIFKQV-------------YNEISVSIAAGLLLAALQNAGLVTVTTTPLNAGPRLRVLLGRPSHEKLLVLLPVGYPSRDATVPDLKRKALDQIMVTVH 286
                                    77        87        97       107       117       127       137       147       | -         -         -|      187      |  -         -|      217       227       237       247       257       267       277         
                                                                                                                 155                    178             194           208                                                                              


Chain B from PDB  Type:PROTEIN  Length:185
 aligned with IYD1_MOUSE | Q9DCX8 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:220
                                                                                                                                                                                                                                                   285  
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       | -
           IYD1_MOUSE    68 EHIPFSHTRYPEQEMRMRSQEFYELLNKRRSVRFISSEHVPMEVIENVIKAAGTAPSGAHTEPWTFVVVKDPDMKHKIREIIEEEEEINYMKRMGKRWVTDLKKLRTNWIKEYLDTAPVLILIFKQVHGFAANGKKKVHYYNEISVSIACGLLLAALQNAGLVTVTTTPLNCGPRLRVLLGRPSHEKLLVLLPVGYPSRDATVPDLKRKALDQIMVTV--   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee......hhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhh...hhhhh..eeeeee.hhhhhhhhhhhhhhh...----------------------.hhhhhh.eeeeeeee.-------------.hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh....eeeeeeeee.......eee.....hhhh.eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3to0 B  68 EHIPFSHTRYPEQEMRMRSQEFYELLNKRRSVRFISSEHVPMEVIENVIKAAGTAPSGAHTEPWTFVVVKDPDMKHKIREIIEEEEEI----------------------KEYLDTAPVLILIFKQV-------------YNEISVSIAAGLLLAALQNAGLVTVTTTPLNAGPRLRVLLGRPSHEKLLVLLPVGYPSRDATVPDLKRKALDQIMVTVHH 287
                                    77        87        97       107       117       127       137       147       | -         -         -|      187      |  -         -|      217       227       237       247       257       267       277       287
                                                                                                                 155                    178             194           208
   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  (0, 0)

(no "SCOP Domain" information available for 3TO0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TO0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TO0)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (IYD1_MOUSE | Q9DCX8)
molecular function
    GO:0004447    iodide peroxidase activity    Catalysis of the reaction: iodide + hydrogen peroxide = iodine + 2 H2O.
    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:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    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:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IYD1_MOUSE | Q9DCX8: 3gb5 3gfd 3gh8 3tnz

(-) Related Entries Specified in the PDB File

3gb5 THE WILD TYPE PROTEIN OF MUS MUSCULUS IODOTYROSINE DEIODINASE (IYD) EXPRESSED IN SF9 BOUND TO FMN
3gfd THE WILD TYPE PROTEIN OF M. MUSCULUS IYD EXPRESSED IN SF9 BOUND TO FMN AND MONO-IODOTYROSINE (MIT)
3gh8 THE WILD TYPE PROTEIN OF M. MUSCULUS IYD EXPRESSED IN SF9 BOUND TO FMN AND DI-IODOTYROSINE (DIT)
3tnz THE C217A, C239A MUTANT PROTEIN OF M. MUSCULUS IYD BOUND TO FMN AND MIT