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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FAT MASS AND OBESITY ASSOCIATED (FTO) PROTEIN REVEALS BASIS FOR ITS SUBSTRATE SPECIFICITY
 
Authors :  J. Chai, Z. Han
Date :  18 Jan 10  (Deposition) - 07 Apr 10  (Release) - 28 Apr 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Fat Mass And Obesity Associated (Fto) Protein, Fe2+/2-Oxoglutarate (2-Og)-Dependent Oxidative Dna/Rna Demethylases, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. Han, T. Niu, J. Chang, X. Lei, M. Zhao, Q. Wang, W. Cheng, J. Wang, Y. Feng, J. Chai
Crystal Structure Of The Fto Protein Reveals Basis For Its Substrate Specificity
Nature V. 464 1205 2010
PubMed-ID: 20376003  |  Reference-DOI: 10.1038/NATURE08921

(-) Compounds

Molecule 1 - PROTEIN FTO
    ChainsA
    EC Number1.14.11.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 32-505
    GeneFTO
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymFAT MASS AND OBESITY-ASSOCIATED PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
13DT1Ligand/Ion3-METHYLTHYMIDINE
2FE21Ligand/IonFE (II) ION
3OGA1Ligand/IonN-OXALYLGLYCINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:96 , TYR A:106 , TYR A:108 , LEU A:109 , VAL A:228 , HIS A:231 , HIS A:232 , ASP A:233 , GLU A:234 , ARG A:322 , OGA A:1550BINDING SITE FOR RESIDUE 3DT A 506
2AC2SOFTWAREARG A:96 , ASN A:205 , HIS A:231 , ASP A:233 , VAL A:244 , TYR A:295 , HIS A:307 , ARG A:316 , SER A:318 , THR A:320 , ARG A:322 , 3DT A:506 , FE2 A:507BINDING SITE FOR RESIDUE OGA A 1550
3AC3SOFTWAREHIS A:231 , ASP A:233 , HIS A:307 , OGA A:1550BINDING SITE FOR RESIDUE FE2 A 507

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asp A:208 -Pro A:209
2Arg A:473 -Pro A:474

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Asymmetric/Biological Unit (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_076423H271PFTO_HUMANUnclassified  ---AH271P
2UniProtVAR_063252R316QFTO_HUMANDisease (GDFD)121918214AR316Q
3UniProtVAR_075468S319FFTO_HUMANDisease (GDFD)  ---AS319F
4UniProtVAR_075469R322QFTO_HUMANDisease (GDFD)745616565AR322Q
5UniProtVAR_032078A405VFTO_HUMANPolymorphism16952624AA405V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LFM)

(-) 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:420
 aligned with FTO_HUMAN | Q9C0B1 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:495
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494     
            FTO_HUMAN     5 PTAEEREREAKKLRLLEELEDTWLPYLTPKDDEFYQQWQLKYPKLILREASSVSEELHKEVQEAFLTLHKHGCLFRDLVRIQGKDLLTPVSRILIGNPGCTYKYLNTRLFTVPWPVKGSNIKHTEAEIAAACETFLKLNDYLQIETIQALEELAAKEKANEDAVPLCMSADFPRVGMGSSYNGQDEVDIKSRAAYNVTLLNFMDPQKMPYLKEEPYFGMGKMAVSWHHDENLVDRSAVAVYSYSCEGPEEESEDDSHLEGRDPDIWHVGFKISWDIETPGLAIPLHQGDCYFMLDDLNATHQHCVLAGSQPRFSSTHRVAECSTGTLDYILQRCQLALQNVCDDVDNDDVSLKSFEPAVLKQGEEIHNEVEFEWLRQFWFQGNRYRKCTDWWCQPMAQLEALWKKMEGVTNAVLHEVKREGLPVEQRNEILTAILASLTARQNLRREWHARCQSRIARTLPADQKPECRPYWEKDDASMPLPFDLTDIVSELRGQ 499
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---                     ------FTO_NTD-3lfmA01 A:35-326                                                                                                                                                                                                                                                                            --FTO_CTD-3lfmA02 A:329-499                                                                                                                                                   Pfam domains
         Sec.struct. author ...---------------------.ee....hhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhhh......eehhhhh.ee...eeeeee....eeee..eeee.ee....--------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-----------------------------hhhhhhhhh...eeeeeee..................eeeeee..........eeeeeee..-------------......eeeeeee.......eeeeee....eeee..hhhhheeeeee.....eeeeeee.......hhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..---..........hhhhhhhhhhhhhhhhhhhh.hhhhh-..........................hhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P--------------------------------------------Q--F--Q----------------------------------------------------------------------------------V---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lfm A  26 PRG---------------------SHMTPKDDEFYQQWQLKYPKLILREASSVSEELHKEVQEAFLTLHKHGCLFRDLVRIQGKDLLTPVSRILIGNPGCTYKYLNTRLFTVPWPVK--------AEIAAACETFLKLNDYLQIETIQALEELAA-----------------------------DEVDIKSRAAYNVTLLNFMDPQKMPYLKEEPYFGMGKMAVSWHHDENLVDRSAVAVYSYSCE-------------GRDPDIWHVGFKISWDIETPGLAIPLHQGDCYFMLDDLNATHQHCVLAGSQPRFSSTHRVAECSTGTLDYILQRCQLALQNVCDDVDNDDVSLKSFEPAVLKQGEEIHNEVEFEWLRQFWFQGNRYRKCTDWWCQPMAQLEALWKKMEGVTNAVLHEVKRE---VEQRNEILTAILASLTARQNLRREWHARCQSRIART-PADQKPECRPYWEKDDASMPLPFDLTDIVSELRGQ 499
                              |      -         -    |   34        44        54        64        74        84        94       104       114      |  -     | 134       144       154    |    -         -         -    |  194       204       214       224       234       244     |   -       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424   |   434       444       454        |-|      474       484       494     
                             28                    29                                                                                         121      130                          159                           189                                                          250           264                                                                                                                                                             424 428                                463 |                                  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      465                                  

   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 3LFM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FTO_HUMAN | Q9C0B1)
molecular function
    GO:0043734    DNA-N1-methyladenine dioxygenase activity    Catalysis of the oxidative demethylation of N1-methyladenine and N3-methylcytosine in DNA, with concomitant decarboxylation of 2-oxoglutarate and releases oxidized methyl group on N1-methyladenine and N3-methylcytosine as formaldehyde.
    GO:1990931    RNA N6-methyladenosine dioxygenase activity    Catalysis of the oxidative demethylation of N6-methyladenosine RNA, with concomitant decarboxylation of 2-oxoglutarate and releases oxidized methyl group on N6-methyladenosine as formaldehyde.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0035516    oxidative DNA demethylase activity    Catalysis of the removal of the methyl group from one or more nucleotides within a DNA molecule involving the oxidation (i.e. electron loss) of one or more atoms.
    GO:0035515    oxidative RNA demethylase activity    Catalysis of the removal of a methyl group from one or more nucleosides within a RNA molecule involving the oxidation (i.e. electron loss) of one or more atoms.
    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:0006307    DNA dealkylation involved in DNA repair    The repair of alkylation damage, e.g. the removal of the alkyl group at the O6-position of guanine by O6-alkylguanine-DNA alkyltransferase (AGT).
    GO:0080111    DNA demethylation    The removal of a methyl group from one or more nucleotides within an DNA molecule.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0042245    RNA repair    Any process that results in the repair of damaged RNA.
    GO:0060612    adipose tissue development    The process whose specific outcome is the progression of adipose tissue over time, from its formation to the mature structure. Adipose tissue is specialized tissue that is used to store fat.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    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:0070989    oxidative demethylation    The process of removing one or more methyl groups from a molecule, involving the oxidation (i.e. electron loss) of one or more atoms in the substrate.
    GO:0035552    oxidative single-stranded DNA demethylation    Removal of the methyl group from one or more nucleotides within a single-stranded DNA molecule involving the oxidation (i.e. electron loss) of one or more atoms.
    GO:0035553    oxidative single-stranded RNA demethylation    Removal of the methyl group from one or more nucleotides within a single-stranded RNA molecule involving the oxidation (i.e. electron loss) of one or more atoms.
    GO:0090335    regulation of brown fat cell differentiation    Any process that modulates the rate, frequency, or extent of brown fat cell differentiation. Brown fat cell differentiation is the process in which a relatively unspecialized cell acquires specialized features of a brown adipocyte, an animal connective tissue cell involved in adaptive thermogenesis. Brown adipocytes contain multiple small droplets of triglycerides and a high number of mitochondria.
    GO:0010883    regulation of lipid storage    Any process that modulates the rate, frequency or extent of lipid storage. Lipid storage is the accumulation and maintenance in cells or tissues of lipids, compounds soluble in organic solvents but insoluble or sparingly soluble in aqueous solvents. Lipid reserves can be accumulated during early developmental stages for mobilization and utilization at later stages of development.
    GO:0040014    regulation of multicellular organism growth    Any process that modulates the frequency, rate or extent of growth of the body of an organism so that it reaches its usual body size.
    GO:0044065    regulation of respiratory system process    Any process that modulates the frequency, rate or extent of a respiratory system process, an organ system process carried out by any of the organs or tissues of the respiratory system.
    GO:0070350    regulation of white fat cell proliferation    Any process that modulates the frequency, rate or extent of white fat cell proliferation.
    GO:0001659    temperature homeostasis    A homeostatic process in which an organism modulates its internal body temperature.
cellular component
    GO:0016607    nuclear speck    A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FTO_HUMAN | Q9C0B14cxw 4cxx 4cxy 4idz 4ie0 4ie4 4ie5 4ie6 4ie7 4qho 4qkn 4zs2 4zs3 5dab 5f8p

(-) Related Entries Specified in the PDB File

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