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(-) Description

Title :  NGTET1 IN COMPLEX WITH 5HMC DNA
 
Authors :  H. Hashimoto, J. E. Pais, N. Dai, X. Zhang, Y. Zheng, X. Cheng
Date :  09 Jul 15  (Deposition) - 09 Sep 15  (Release) - 23 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dioxygenase, 5-Hydroxymethylcytosine, Ngtet1, Oxidoreductase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Hashimoto, J. E. Pais, N. Dai, I. R. Correa, X. Zhang, Y. Zheng, X. Cheng
Structure Of Naegleria Tet-Like Dioxygenase (Ngtet1) In Complexes With A Reaction Intermediate 5-Hydroxymethylcytosine Dna.
Nucleic Acids Res. V. 43 10713 2015
PubMed-ID: 26323320  |  Reference-DOI: 10.1093/NAR/GKV870

(-) Compounds

Molecule 1 - TET-LIKE DIOXYGENASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B-HIS-SUMO
    Expression System Strain: BL21(DE3) CODON PLUS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 57-321
    Gene: NAEGRDRAFT_55029
    Organism Common: AMOEBA
    Organism Scientific: NAEGLERIA GRUBERI
    Organism Taxid: 5762
 
Molecule 2 - DNA (5'-D(*AP*GP*AP*AP*TP*TP*CP*CP*GP*TP*TP*CP*CP*A)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*TP*GP*GP*AP*AP*(5HC)P*GP*GP*AP*AP*TP*TP*CP*T)- 3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
15HC1Mod. Nucleotide2'-DEOXY-5-(HYDROXYMETHYL)CYTIDINE 5'-(DIHYDROGENPHOSPHATE)
2AKG1Ligand/Ion2-OXOGLUTARIC ACID
3MN1Ligand/IonMANGANESE (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:214 , ARG A:224 , HIS A:229 , ASP A:231 , TYR A:242 , LEU A:253 , HIS A:279 , VAL A:281 , ARG A:289 , MN A:402 , HOH A:501 , 5HC C:20binding site for residue AKG A 401
2AC2SOFTWAREHIS A:229 , ASP A:231 , HIS A:279 , AKG A:401 , HOH A:501binding site for residue MN A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CG8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5CG8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CG8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CG8)

(-) Exons   (0, 0)

(no "Exon" information available for 5CG8)

(-) 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:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh......eeee.......ee...eeee.....eeeeee....hhhhhhhhhhhhhhhhhh....eeeeeee......eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeee.....................eeeeeeee.......eee....eee......eeee......eee......eeeeeeee..hhhhhh.eeeeehhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cg8 A  56 MINKKSLLQNLLSKCKTTFQQSFTNANITLKDEKWLKNVRTAYFVCDHDGSVELAYLPNVLPKELVEEFTEKFESIQTGRKKDTGYSGILDNSMPFNYVTADLSQELGQYLSEIVNPQINYYISKLLTCVSSRTINYLVSLNDSYYALNNCLYPSTAFNSLKPSNDGHRIRKPHKDNLDITPSSLFYFGNFQNTEGYLELTDKNCKVFVQPGDVLFFKGNEYKHVVANITSGWRIGLVYFAHKGSKTKPYYEDTQKNSLKIHKETK 321
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315      


Chain B from PDB  Type:DNA  Length:14
                                              
                 5cg8 B   1 AGAATTCCGTTCCA  14
                                    10    


Chain C from PDB  Type:DNA  Length:14
                                              
                 5cg8 C  15 TGGAAxGGAATTCT  28
                                 |  24    
                                20-5HC
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  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 5CG8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CG8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CG8)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        D2W6T1_NAEGR | D2W6T1: 4lt5 5cg9

(-) Related Entries Specified in the PDB File

5cg9