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(-) Description

Title :  CRYSTAL STRUCTURE OF TET2-DNA COMPLEX
 
Authors :  L. Hu, Z. Li, J. Cheng, Q. Rao, W. Gong, M. Liu, P. Wang, Y. Xu
Date :  14 Nov 13  (Deposition) - 18 Dec 13  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.03
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dna Hydroxylation, Oxidoreductase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Hu, Z. Li, J. Cheng, Q. Rao, W. Gong, M. Liu, Y. G. Shi, J. Zhu, P. Wang, Y. Xu
Crystal Structure Of Tet2-Dna Complex: Insight Into Tet-Mediated 5Mc Oxidation.
Cell(Cambridge, Mass. ) V. 155 1545 2013
PubMed-ID: 24315485  |  Reference-DOI: 10.1016/J.CELL.2013.11.020

(-) Compounds

Molecule 1 - METHYLCYTOSINE DIOXYGENASE TET2
    Chains: A
    EC Number: 1.14.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: SEE REMARK 999
    Gene: TET2, KIAA1546, NBLA00191
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - 5'-D(*AP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*T)-3'
    Chains: B, C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
15CM2Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2FE21Ligand/IonFE (II) ION
3OGA1Ligand/IonN-OXALYLGLYCINE
4ZN3Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:1193 , CYS A:1271 , CYS A:1273 , HIS A:1380BINDING SITE FOR RESIDUE ZN A 2001
2AC2SOFTWARECYS A:1133 , CYS A:1135 , HIS A:1219 , CYS A:1221BINDING SITE FOR RESIDUE ZN A 2002
3AC3SOFTWARECYS A:1289 , CYS A:1298 , CYS A:1358 , HIS A:1912BINDING SITE FOR RESIDUE ZN A 2003
4AC4SOFTWAREHIS A:1382 , ASP A:1384 , HIS A:1881 , OGA A:2005 , HOH A:2149BINDING SITE FOR RESIDUE FE2 A 2004
5AC5SOFTWAREARG 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 , FE2 A:2004 , HOH A:2142 , HOH A:2149 , 5CM B:6BINDING SITE FOR RESIDUE OGA A 2005

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NM6)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Leu A:1151 -Gly A:1152
2Gln A:1191 -Gly A:1192
3Glu A:1411 -Asp A:1412
4Leu A:1447 -Ser A:1448

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NM6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NM6)

(-) Exons   (0, 0)

(no "Exon" information available for 4NM6)

(-) 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:407
                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............ee.hhhhhhhhhhhhhh.hhh.eeeeeeee...............eee........eeeeeee.........eeeeeeee....hhhhhhhhhhhhhhhhhhhh....hhhhh.................eeeeee..ee....ee................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh..........eeeeee.................eeeeeee.hhhh...........eee..eee.......hhhhhhhhhhhh.eee....eeeeeee.......eeeeeeehhhhhhh.....eee......eeee.......ee............eeeeeee......hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4nm6 A 1132 SCRCEGPFYTHLGAGPNVAAIREIMEERFGQKGKAIRIERVIYTGKEGKSSQGCPIAKWVVRRSSSEEKLLCLVRERAGHTCEAAVIVILILVWEGIPLSLADKLYSELTETLRKYGTLTNRRCALNEERTCACQGLDPETCGASFSFGCSWSMYYNGCKFARSKIPRKFKLLGDDPKEEEKLESHLQNLSTLMAPTYKKLAPDAYNNQIEYEHRAPECRLGLKEGRPFSGVTACLDFCAHAHRDLHNMQNGSTLVCTLTREDNREFGGKPEDEQLHVLPLYKVSDVDEFGSVEAQEEKKRSGAIQVLSSFRRKVRMLAEPVKTGSDEVWSDSEQSFLDPDIGGVAVAPTHGSILIECAKRELHATTPLKNPNRNHPTRISLVFYQHKSMNEPKHGLALWEAKMAEK 1924
                               || 1149      1159      1169      1179      1189      1199      1209      1219      1229      1239      1249      1259      1269      1279      1289      1299      1309      1319      1329      1339      1349      1359      1369      1379      1389      1399      1409      1419      1429      1439      1449      1459   || 1847      1857      1867      1877      1887      1897      1907      1917       
                               ||                                                                                                                                                                                                                                                                                                                           1463|                                                                                  
                            1135|                                                                                                                                                                                                                                                                                                                            1842                                                                                  
                             1144                                                                                                                                                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:DNA  Length:11
                                            
                4nm6 B    1 ACCACcGGTGG   11
                                 |  10 
                                 6-5CM 


Chain C from PDB  Type:DNA  Length:10
                                           
                4nm6 C    3 CACcGGTGGT   12
                               |    12
                               6-5CM
   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 4NM6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NM6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NM6)

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gln A:1191 - Gly A:1192   [ RasMol ]  
    Glu A:1411 - Asp A:1412   [ RasMol ]  
    Leu A:1151 - Gly A:1152   [ RasMol ]  
    Leu A:1447 - Ser A:1448   [ RasMol ]  
 

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  4nm6
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  TET2_HUMAN | Q6N021
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  1.14.11.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        TET2_HUMAN | Q6N021: 5d9y 5deu

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4NM6)