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(-) Description

Title :  CRYSTAL STRUCTURE OF MUS MUSCULUS IODOTYROSINE DEIODINASE (IYD) BOUND TO FMN AND MONO-IODOTYROSINE (MIT)
 
Authors :  S. R. Thomas, P. M. Mctamney, J. M. Adler, N. Laronde-Leblanc, S. E. Roki
Date :  26 Feb 09  (Deposition) - 12 May 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Iyd, Iodide Salvage, Flavoprotein, Mono-Iodotyrosine, Mit, Fmn, Membrane, Nadp, Oxidoreductase, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. R. Thomas, P. M. Mctamney, J. M. Adler, N. Laronde-Leblanc, S. E. Rokita
Crystal Structure Of Iodotyrosine Deiodinase, A Novel Flavoprotein Responsible For Iodide Salvage In Thyroid Glands.
J. Biol. Chem. V. 284 19659 2009
PubMed-ID: 19436071  |  Reference-DOI: 10.1074/JBC.M109.013458

(-) Compounds

Molecule 1 - IODOTYROSINE DEHALOGENASE 1
    Chains: A, B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Plasmid: PFASTBAC1
    Expression System Taxid: 7108
    Expression System Vector: BACULOVIRUS
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 34-285
    Gene: DEHAL1, IYD
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 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, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
2GOL3Ligand/IonGLYCEROL
3IYR2Ligand/Ion3-IODO-TYROSINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:15 , HOH A:17 , ARG A:96 , ARG A:97 , SER A:98 , ARG A:100 , THR A:174 , VAL A:232 , THR A:233 , THR A:235 , ARG A:275 , IYR A:302 , HOH A:372 , HOH A:395 , PRO B:123 , SER B:124 , GLY B:125 , HOH B:553BINDING SITE FOR RESIDUE FMN A 301
2AC2SOFTWAREGLU A:153 , TYR A:157 , LEU A:169 , THR A:174 , ASN A:175 , LYS A:178 , THR A:235 , FMN A:301 , HOH A:356 , HOH A:400 , GLY B:125 , ALA B:126BINDING SITE FOR RESIDUE IYR A 302
3AC3SOFTWARETYR A:207 , TYR A:208 , HOH A:331 , HOH A:411 , HOH A:415 , HOH A:462 , TRP B:165BINDING SITE FOR RESIDUE GOL A 1
4AC4SOFTWAREARG A:76 , TYR A:77 , GLU A:81 , TYR A:157 , MET A:158 , VAL A:166 , LYS A:170BINDING SITE FOR RESIDUE GOL A 3
5AC5SOFTWAREPRO A:123 , SER A:124 , GLY A:125 , TYR A:208 , ILE A:211 , ILE A:215 , HOH A:416 , HOH B:13 , ARG B:96 , ARG B:97 , SER B:98 , ARG B:100 , LEU B:172 , VAL B:232 , THR B:233 , THR B:234 , THR B:235 , LEU B:273 , ARG B:275 , IYR B:302 , HOH B:308 , HOH B:333 , HOH B:550BINDING SITE FOR RESIDUE FMN B 301
6AC6SOFTWAREGLY A:125 , ALA A:126 , TYR A:207 , GLU B:153 , TYR B:157 , MET B:161 , LEU B:169 , LEU B:172 , ASN B:175 , LYS B:178 , THR B:235 , FMN B:301 , HOH B:314 , HOH B:320BINDING SITE FOR RESIDUE IYR B 302
7AC7SOFTWARELEU A:237 , TYR B:207 , TYR B:208 , HOH B:532BINDING SITE FOR RESIDUE GOL B 2

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:66 -Val A:67
2Val B:285 -His B:286

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3GFD)

(-) 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:220
 aligned with IYD1_MOUSE | Q9DCX8 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:222
                                                                                                                                                                                                                                                     285  
                                    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285  
           IYD1_MOUSE    66 SVEHIPFSHTRYPEQEMRMRSQEFYELLNKRRSVRFISSEHVPMEVIENVIKAAGTAPSGAHTEPWTFVVVKDPDMKHKIREIIEEEEEINYMKRMGKRWVTDLKKLRTNWIKEYLDTAPVLILIFKQVHGFAANGKKKVHYYNEISVSIACGLLLAALQNAGLVTVTTTPLNCGPRLRVLLGRPSHEKLLVLLPVGYPSRDATVPDLKRKALDQIMVTV--   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee......hhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh...hhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhh.eeeeeeee.ee.--....ee..hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhh.....eeeeeeeee.......eee.....hhhh.eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gfd A  66 SVEHIPFSHTRYPEQEMRMRSQEFYELLNKRRSVRFISSEHVPMEVIENVIKAAGTAPSGAHTEPWTFVVVKDPDMKHKIREIIEEEEEINYMKRMGKRWVTDLKKLRTNWIKEYLDTAPVLILIFKQVHGF--NGKKKVHYYNEISVSIACGLLLAALQNAGLVTVTTTPLNCGPRLRVLLGRPSHEKLLVLLPVGYPSRDATVPDLKRKALDQIMVTVHH 287
                                    75        85        95       105       115       125       135       145       155       165       175       185       195 |  |  205       215       225       235       245       255       265       275       285  
                                                                                                                                                             197  |                                                                                       
                                                                                                                                                                200                                                                                       


Chain B from PDB  Type:PROTEIN  Length:219
 aligned with IYD1_MOUSE | Q9DCX8 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:221
                                                                                                                                                                                                                                                     285 
                                    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285 
           IYD1_MOUSE    66 SVEHIPFSHTRYPEQEMRMRSQEFYELLNKRRSVRFISSEHVPMEVIENVIKAAGTAPSGAHTEPWTFVVVKDPDMKHKIREIIEEEEEINYMKRMGKRWVTDLKKLRTNWIKEYLDTAPVLILIFKQVHGFAANGKKKVHYYNEISVSIACGLLLAALQNAGLVTVTTTPLNCGPRLRVLLGRPSHEKLLVLLPVGYPSRDATVPDLKRKALDQIMVTV-   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee......hhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh...hhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhh.eeeeeeee.ee.--....ee..hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhh.....eeeeeeeee.......eee.....hhhhheeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gfd B  66 SVEHIPFSHTRYPEQEMRMRSQEFYELLNKRRSVRFISSEHVPMEVIENVIKAAGTAPSGAHTEPWTFVVVKDPDMKHKIREIIEEEEEINYMKRMGKRWVTDLKKLRTNWIKEYLDTAPVLILIFKQVHGF--NGKKKVHYYNEISVSIACGLLLAALQNAGLVTVTTTPLNCGPRLRVLLGRPSHEKLLVLLPVGYPSRDATVPDLKRKALDQIMVTVH 286
                                    75        85        95       105       115       125       135       145       155       165       175       185       195 |  |  205       215       225       235       245       255       265       275       285 
                                                                                                                                                             197  |                                                                                      
                                                                                                                                                                200
   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 3GFD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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)

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        IYD1_MOUSE | Q9DCX8: 3gb5 3gh8 3tnz 3to0

(-) Related Entries Specified in the PDB File

3gb5 CRYSTAL STRUCTURE OF MUS MUSCULUS IODOTYROSINE DEIODINASE (IYD) BOUND TO FMN
3gh8 CRYSTAL STRUCTURE OF MUS MUSCULUS IODOTYROSINE DEIODINASE (IYD) BOUND TO FMN AND DI-IODOTYROSINE (DIT)