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(-) Description

Title :  CRYSTAL STRUCTURE OF DOT1L IN COMPLEX WITH A BROMINATED SAH ANALOG
 
Authors :  W. Yu, W. Tempel, D. Smil, M. Schapira, Y. Li, M. Vedadi, K. T. Nguyen, A. K. Wernimont, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigel P. J. Brown, Structural Genomics Consortium (Sgc)
Date :  14 Jul 11  (Deposition) - 27 Jul 11  (Release) - 27 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
Chains :  Asym./Biol. Unit :  A
Keywords :  Histone, Methyltransferase, Epigenetics, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Yu, W. Tempel, D. Smil, M. Schapira, Y. Li, M. Vedadi, K. T. Nguyen, A. K. Wernimont, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, P. J. Brown
Crystal Structure Of Dot1L In Complex With A Brominated Sah Analog
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC
    ChainsA
    EC Number2.1.1.43
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28-MHL
    Expression System StrainBL21-V2R-PRARE2
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentSEQUENCE DATABASE RESIDUES 1-420
    GeneDOT1L, KIAA1814, KMT4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDOT1-LIKE PROTEIN, HISTONE H3-K79 METHYLTRANSFERASE, H3-K79- HMTASE, LYSINE N-METHYLTRANSFERASE 4

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 22)

Asymmetric/Biological Unit (3, 22)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2SX01Ligand/Ion(2S)-2-AMINO-4-({[(2S,3S,4R,5R)-5-(4-AMINO-5-BROMO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL}SULFANYL)BUTANOICACID (NON-PREFERRED NAME)
3UNX20Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:133 , GLY A:137 , GLU A:138 , THR A:139 , ASP A:161 , GLY A:163 , SER A:164 , GLN A:168 , GLU A:186 , LYS A:187 , GLY A:221 , ASP A:222 , PHE A:223 , PHE A:239 , ASN A:241 , PHE A:245 , HOH A:443 , HOH A:459BINDING SITE FOR RESIDUE SX0 A 421
2AC2SOFTWAREARG A:203 , LYS A:207 , HIS A:213 , HOH A:470BINDING SITE FOR RESIDUE SO4 A 422

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SX0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp A:22 -Pro A:23

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SX0)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DOT1PS51569 Histone-lysine N-methyltransferase DOT1 (EC 2.1.1.43) domain profile.DOT1L_HUMAN16-330  1A:16-330

(-) Exons   (0, 0)

(no "Exon" information available for 3SX0)

(-) 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:324
 aligned with DOT1L_HUMAN | Q8TEK3 from UniProtKB/Swiss-Prot  Length:1739

    Alignment length:329
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323         
          DOT1L_HUMAN     4 KLELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMENYVLIDYDTKSFESMQRLCDKYNRAIDSIHQLWKGTTQPMKLNTRPSTGLLRHILQQVYNHSVTDPEKLNNYEPFSPEVYGETSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKGSVSWTGKPVSYYLHTIDRTILENYFSSLKNP 332
               SCOP domains d3sx0a_ A: automated matches                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee........eeee..........hhhhhhhhhhhhhhhhhhhhhhhhh-----.....hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhh.hhhhhhh............hhhhhhhhhhhhh.....eeeee....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhh..eeee.....hhhhhhhhhhhhh......eeee.................hhhh.eeeee.................eeeee.hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------DOT1  PDB: A:16-330 UniProt: 16-330                                                                                                                                                                                                                                                                                        -- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sx0 A   4 KLELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAME-----DYDTKSFESMQRLCDKYNRAIDSIHQLWKGTTQPMKLNTRPSTGLLRHILQQVYNHSVTDPEKLNNYEPFSPEVYGETSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKGSVSWTGKPVSYYLHTIDRTILENYFSSLKNP 332
                                    13        23        33        43        53  |     63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323         
                                                                               56    62                                                                                                                                                                                                                                                                              

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SX0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SX0)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DOT1L_HUMAN | Q8TEK3)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0042054    histone methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + histone = S-adenosyl-L-homocysteine + methyl-histone. Histone methylation generally occurs on either an arginine or lysine residue.
    GO:0031151    histone methyltransferase activity (H3-K79 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 79) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 79). This reaction is the addition of a methyl group onto lysine at position 79 of the histone H3 protein.
    GO:0018024    histone-lysine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine. The methylation of peptidyl-lysine in histones forms N6-methyl-L-lysine, N6,N6-dimethyl-L-lysine and N6,N6,N6-trimethyl-L-lysine derivatives.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006342    chromatin silencing    Repression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin.
    GO:0034729    histone H3-K79 methylation    The modification of histone H3 by addition of a methyl group to lysine at position 79 of the histone.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0046425    regulation of JAK-STAT cascade    Any process that modulates the frequency, rate or extent of the JAK-STAT signaling pathway.
    GO:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.
    GO:2000677    regulation of transcription regulatory region DNA binding    Any process that modulates the frequency, rate or extent of transcription regulatory region DNA binding.
    GO:0032200    telomere organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of telomeres, terminal regions of a linear chromosome that include the telomeric DNA repeats and associated proteins.
cellular component
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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
        DOT1L_HUMAN | Q8TEK31nw3 2mv7 3qow 3qox 3sr4 3uwp 4ek9 4ekg 4eki 4eqz 4er0 4er3 4er5 4er6 4er7 4hra 4wvl 5drt 5dry 5dsx 5dt2 5dtm 5dtq 5dtr 5juw 5mvs 5mw3 5mw4

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