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(-) Description

Title :  CRYSTAL STRUCTURE OF TET2-5HMC COMPLEX
 
Authors :  L. Hu, J. Cheng, Q. Rao, Z. Li, J. Li, Y. Xu
Date :  26 Aug 15  (Deposition) - 04 Nov 15  (Release) - 18 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  5-Methylcytosine Dioxygenase, Tet2, 5Hmc, Protein-Dna Complex, Oxidoreductase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Hu, J. Lu, J. Cheng, Q. Rao, Z. Li, H. Hou, Z. Lou, L. Zhang, W. Li, W. Gong, M. Liu, C. Sun, X. Yin, J. Li, X. Tan, P. Wang, Y. Wang, D. Fang, Q. Cui, P. Yang, C. He, H. Jiang, C. Luo, Y. Xu
Structural Insight Into Substrate Preference For Tet-Mediated Oxidation.
Nature V. 527 118 2015
PubMed-ID: 26524525  |  Reference-DOI: 10.1038/NATURE15713

(-) Compounds

Molecule 1 - METHYLCYTOSINE DIOXYGENASE TET2, CHIMERIC CONSTRUCT
    ChainsA
    EC Number1.14.11.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 1129-1480, 1844-1935
    GeneTET2, KIAA1546, NBLA00191
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - DNA (5'-D(*AP*CP*CP*AP*CP*(5HC)P*GP*GP*TP*GP*GP*T)-3')
    ChainsB
    EngineeredYES
    Expression SystemSYNTHETIC CONSTRUCT
    Expression System Taxid32630
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
 
Molecule 3 - DNA (5'-D(P*CP*CP*AP*CP*(5HC)P*GP*GP*TP*GP*GP*T)-3')
    ChainsC
    EngineeredYES
    Expression SystemSYNTHETIC CONSTRUCT
    Expression System Taxid32630
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 9)

Asymmetric/Biological Unit (6, 9)
No.NameCountTypeFull Name
15HC2Mod. Nucleotide2'-DEOXY-5-(HYDROXYMETHYL)CYTIDINE 5'-(DIHYDROGENPHOSPHATE)
2CL1Ligand/IonCHLORIDE ION
3FE1Ligand/IonFE (III) ION
4MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5OGA1Ligand/IonN-OXALYLGLYCINE
6ZN3Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:1261 , CYS A:1374 , HIS A:1382 , ASP A:1384 , HIS A:1416 , HIS A:1881 , THR A:1883 , ARG A:1896 , SER A:1898 , FE A:2003 , HOH A:2113 , 5HC B:6binding site for residue OGA A 2001
2AC2SOFTWAREGLU A:1186 , ALA A:1381 , HIS A:1382 , ARG A:1383 , LEU A:1385 , LEU A:1880 , HOH A:2111 , DG C:11binding site for residue MES A 2002
3AC3SOFTWAREHIS A:1382 , ASP A:1384 , HIS A:1881 , OGA A:2001 , HOH A:2113binding site for residue FE A 2003
4AC4SOFTWARECYS A:1133 , CYS A:1135 , HIS A:1219 , CYS A:1221binding site for residue ZN A 2004
5AC5SOFTWARECYS A:1193 , CYS A:1271 , CYS A:1273 , HIS A:1380binding site for residue ZN A 2005
6AC6SOFTWARECYS A:1289 , CYS A:1298 , CYS A:1358 , HIS A:1912binding site for residue ZN A 2006
7AC7SOFTWAREASN A:1387 , SER A:1392 , THR A:1393 , ALA A:1876 , LYS A:1877binding site for residue CL A 2007

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DEU)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:1132 -Cys A:1133

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DEU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DEU)

(-) Exons   (0, 0)

(no "Exon" information available for 5DEU)

(-) 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:413
                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh.......ee.hhhhhhhhhhhhhh.hhh.eeeeeeee...............eee........eeeeeee.........eeeeeeee....hhhhhhhhhhhhhhhhhhhh....hhhhh.................eeeeee..ee....ee................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh..........eeeeee.................eeeeeee................eee..eee.......hhhhhhhhhhh..eee....eeeeeee........eeeeeeehhhhhhh.....eee......eeee.......ee............eeeeeee......hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5deu A 1132 SCRCVEQIIEKDEGPFYTHLGAGPNVAAIREIMEERFGQKGKAIRIERVIYTGKEGKSSQGCPIAKWVVRRSSSEEKLLCLVRERAGHTCEAAVIVILILVWEGIPLSLADKLYSELTETLRKYGTLTNRRCALNEERTCACQGLDPETCGASFSFGCSWSMYYNGCKFARSKIPRKFKLLGDDPKEEEKLESHLQNLSTLMAPTYKKLAPDAYNNQIEYEHRAPECRLGLKEGRPFSGVTACLDFCAHAHRDLHNMQNGSTLVCTLTREDNREFGGKPEDEQLHVLPLYKVSDVDEFGSVEAQEEKKRSGAIQVLSSFRRKVRMLAEPVKTCGSDEVWSDSEQSFLDPDIGGVAVAPTHGSILIECAKRELHATTPLKNPNRNHPTRISLVFYQHKSMNEPKHGLALWEAKM 1921
                                  1141      1151      1161      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261      1271      1281      1291      1301      1311      1321      1331      1341      1351      1361      1371      1381      1391      1401      1411      1421      1431      1441      1451      1461  ||  1848      1858      1868      1878      1888      1898      1908      1918   
                                                                                                                                                                                                                                                                                                                                                                     1464|                                                                               
                                                                                                                                                                                                                                                                                                                                                                      1842                                                                               

Chain B from PDB  Type:DNA  Length:12
                                             
                5deu B    1 ACCACxGGTGGT   12
                                 |  10  
                                 6-5HC  

Chain C from PDB  Type:DNA  Length:11
                                            
                5deu C    2 CCACxGGTGGT   12
                                |   11 
                                6-5HC  

   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 5DEU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DEU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DEU)

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ser A:1132 - Cys A:1133   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        TET2_HUMAN | Q6N0214nm6 5d9y

(-) Related Entries Specified in the PDB File

5d9y