3GB5 - JenaLib

Title :   CRYSTAL STRUCTURE OF MUS MUSCULUS IODOTYROSINE DEIODINASE (IYD) BOUND TO FMN

Authors :   S. R. Thomas, P. M. Mctamney, J. M. Adler, N. Laronde-Leblanc, S. E. Roki

Date :   18 Feb 09 (Deposition) - 12 May 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Iyd, Iodide Salvage, Flavoprotein, 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

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:96 , ARG A:97 , SER A:98 , ARG A:100 , PRO A:123 , SER A:124 , GLY A:125 , HIS A:127 , TYR A:208 , SER A:212 , VAL A:232 , THR A:233 , THR A:235 , LEU A:273 , ARG A:275 , ACT A:303 , HOH A:415 , HOH A:416 , HOH A:426 , HOH A:443 , HOH A:492	BINDING SITE FOR RESIDUE FMN A 301
2	AC2	SOFTWARE	SER A:103 , SER A:104 , ARG A:266 , THR A:284 , VAL A:285 , HIS A:286 , ACT A:304 , HOH A:440 , HOH A:457	BINDING SITE FOR RESIDUE PO4 A 302
3	AC3	SOFTWARE	ALA A:126 , FMN A:301 , HOH A:479	BINDING SITE FOR RESIDUE ACT A 303
4	AC4	SOFTWARE	SER A:265 , ARG A:266 , ASP A:267 , HIS A:286 , HIS A:287 , PO4 A:302	BINDING SITE FOR RESIDUE ACT A 304

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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: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 ..........hhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh...hhhhh..eeeeee.hhhhhhhhhhhhhhh...----------------------.hhhhhh.eeeeeeee.-------------hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh.....eeeeeeeee...............hhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gb5 A  68 EHIPFSHTRYPEQEMRMRSQEFYELLNKRRSVRFISSEHVPMEVIENVIKAAGTAPSGAHTEPWTFVVVKDPDMKHKIREIIEEEEEI----------------------KEYLDTAPVLILIFKQV-------------YNEISVSIACGLLLAALQNAGLVTVTTTPLNCGPRLRVLLGRPSHEKLLVLLPVGYPSRDATVPDLKRKALDQIMVTVHH 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)
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	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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

Asymmetric Unit(hide GO term definitions)

Chain A (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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	Cis Peptide Bonds
		Glu A:153 - Glu A:154	[ RasMol ]

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