Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF MUS MUSCULUS IODOTYROSINE DEIODINASE (IYD) C217A, C239A BOUND TO FMN AND MONO-IODOTYROSINE (MIT)
 
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 :  2.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Flavoprotein, Membrane, Transmembrane, Dehalogenase, Iodide Salvage, Fmn, Mono-Iodotyrosine, Mit, 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 DEHALOGENASE 1
    Chains: A, B
    EC Number: 1.22.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32A
    Expression System Strain: ROSETTA 2(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DEHAL1, IYD, 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  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1FLC2Ligand/IonCITRATE ANION
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
3GOL2Ligand/IonGLYCEROL
4IYR2Ligand/Ion3-IODO-TYROSINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:9 , HOH A:11 , HOH A:30 , ARG A:96 , ARG A:97 , SER A:98 , ARG A:100 , LEU A:172 , THR A:174 , VAL A:232 , THR A:233 , THR A:234 , THR A:235 , LEU A:273 , ARG A:275 , IYR A:302 , HOH A:361 , PRO B:123 , SER B:124 , GLY B:125 , HIS B:127 , TYR B:208 , ILE B:211 , SER B:212BINDING 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:334 , ALA B:126BINDING SITE FOR RESIDUE IYR A 302
3AC3SOFTWAREHIS A:106 , PRO A:108 , MET A:109 , HOH A:392 , ARG B:83 , HOH B:396BINDING SITE FOR RESIDUE FLC A 303
4AC4SOFTWARETYR A:207 , TYR A:208 , LEU B:237BINDING SITE FOR RESIDUE GOL A 304
5AC5SOFTWARELEU A:237 , TYR B:207 , TYR B:208BINDING SITE FOR RESIDUE GOL B 304
6AC6SOFTWAREPRO A:123 , SER A:124 , GLY A:125 , HIS A:127 , TYR A:208 , SER A:212 , HOH B:10 , HOH B:20 , ARG B:96 , ARG B:97 , SER B:98 , ARG B:100 , THR B:174 , VAL B:232 , THR B:233 , THR B:234 , THR B:235 , ARG B:275 , HOH B:294 , HOH B:295 , IYR B:302BINDING SITE FOR RESIDUE FMN B 301
7AC7SOFTWAREALA A:126 , GLU B:153 , TYR B:157 , LEU B:169 , THR B:174 , ASN B:175 , LYS B:178 , THR B:235 , FMN B:301 , HOH B:354BINDING SITE FOR RESIDUE IYR B 302
8AC8SOFTWAREARG A:83 , HIS B:106 , PRO B:108 , MET B:109 , HOH B:300BINDING SITE FOR RESIDUE FLC B 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3TNZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TNZ)

(-) 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:222
 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.eee.....eee..hhhhhhhhhhhhhhhhhhhh...........hhhhhhhhh.....eeeeeeeee.......eee.....hhhh.eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tnz A  66 SVEHIPFSHTRYPEQEMRMRSQEFYELLNKRRSVRFISSEHVPMEVIENVIKAAGTAPSGAHTEPWTFVVVKDPDMKHKIREIIEEEEEINYMKRMGKRWVTDLKKLRTNWIKEYLDTAPVLILIFKQVHGFAANGKKKVHYYNEISVSIAAGLLLAALQNAGLVTVTTTPLNAGPRLRVLLGRPSHEKLLVLLPVGYPSRDATVPDLKRKALDQIMVTVHH 287
                                    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285  


Chain B from PDB  Type:PROTEIN  Length:221
 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.eee.....eee..hhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhh....eeeeeeeee.......eee.....hhhh.eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tnz B  66 SVEHIPFSHTRYPEQEMRMRSQEFYELLNKRRSVRFISSEHVPMEVIENVIKAAGTAPSGAHTEPWTFVVVKDPDMKHKIREIIEEEEEINYMKRMGKRWVTDLKKLRTNWIKEYLDTAPVLILIFKQVHGFAANGKKKVHYYNEISVSIAAGLLLAALQNAGLVTVTTTPLNAGPRLRVLLGRPSHEKLLVLLPVGYPSRDATVPDLKRKALDQIMVTVH 286
                                    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285
   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 3TNZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    FLC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FMN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IYR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3tnz)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3tnz
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  IYD1_MOUSE | Q9DCX8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.22.1.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  IYD1_MOUSE | Q9DCX8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        IYD1_MOUSE | Q9DCX8: 3gb5 3gfd 3gh8 3to0

(-) 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)
3to0 THE C217A, C239A MUTANT PROTEIN OF M. MUSCULUS IYD BOUND TO FLAVIN MONONUCLEOTIDE (FMN)