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(-) Description

Title :  NGTET1 IN COMPLEX WITH 5MC DNA IN SPACE GROUP P3221
 
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 :  2.69
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Dioxygenase, 5-Methylcytosine, 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, D
    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(P*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3')
    Chains: B, E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*TP*GP*TP*CP*AP*GP*(5CM)P*GP*CP*AP*TP*GP*G)-3')
    Chains: C, F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 11)

Asymmetric Unit (5, 11)
No.NameCountTypeFull Name
15CM2Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2AKG2Ligand/Ion2-OXOGLUTARIC ACID
3EDO2Ligand/Ion1,2-ETHANEDIOL
4MN2Ligand/IonMANGANESE (II) ION
5SO43Ligand/IonSULFATE ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
15CM1Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2AKG1Ligand/Ion2-OXOGLUTARIC ACID
3EDO-1Ligand/Ion1,2-ETHANEDIOL
4MN-1Ligand/IonMANGANESE (II) ION
5SO41Ligand/IonSULFATE ION
Biological Unit 2 (4, 6)
No.NameCountTypeFull Name
15CM1Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2AKG1Ligand/Ion2-OXOGLUTARIC ACID
3EDO2Ligand/Ion1,2-ETHANEDIOL
4MN-1Ligand/IonMANGANESE (II) ION
5SO42Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:168 , ALA A:202 , ASN A:205 , EDO D:403binding site for residue SO4 A 401
02AC2SOFTWAREASN A:214 , ARG A:224 , HIS A:229 , ASP A:231 , LEU A:240 , TYR A:242 , LEU A:253 , HIS A:279 , VAL A:281 , ARG A:289 , VAL A:293 , MN A:403 , HOH A:501 , 5CM C:20binding site for residue AKG A 402
03AC3SOFTWAREHIS A:229 , ASP A:231 , HIS A:279 , AKG A:402 , HOH A:501binding site for residue MN A 403
04AC4SOFTWAREASN A:175 , TYR A:201 , ASN A:205 , ASN D:175 , TYR D:201binding site for residue SO4 D 401
05AC5SOFTWAREGLU D:168 , ALA D:202 , ASN D:205 , EDO D:403binding site for residue SO4 D 402
06AC6SOFTWARESO4 A:401 , SO4 D:402binding site for residue EDO D 403
07AC7SOFTWAREASN D:214 , ARG D:224 , HIS D:229 , ASP D:231 , LEU D:240 , TYR D:242 , LEU D:253 , HIS D:279 , VAL D:281 , ARG D:289 , VAL D:293 , MN D:405 , HOH D:501 , 5CM F:20binding site for residue AKG D 404
08AC8SOFTWAREHIS D:229 , ASP D:231 , HIS D:279 , AKG D:404 , HOH D:501binding site for residue MN D 405
09AC9SOFTWAREDG E:8 , DA F:18 , DG F:19binding site for residue EDO F 101
10AD1SOFTWARETYR D:141 , ASN D:147 , ARG D:224 , ASP D:234 , VAL D:293 , PHE D:295 , HIS D:297 , AKG D:404 , DG E:8 , DC E:9 , DT E:10 , DA F:18 , DG F:21 , EDO F:101binding site for Di-nucleotide DG F 19 and 5CM F 20
11AD2SOFTWARETYR D:141 , ASN D:147 , TYR D:153 , ARG D:224 , ASP D:234 , VAL D:293 , PHE D:295 , HIS D:297 , GLN D:310 , AKG D:404 , DG E:6 , DC E:7 , DG F:19 , DC F:22binding site for Di-nucleotide 5CM F 20 and DG F 21

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CG9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5CG9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CG9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CG9)

(-) Exons   (0, 0)

(no "Exon" information available for 5CG9)

(-) Sequences/Alignments

Asymmetric 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:267
                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh......eeee.......ee...eeee.....eeeeee....hhhhhhhhhhhhhhhhhh....eeeeeee.......ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeee......hhhhh..........eeeeeeee.......eee....eee......eeee......eee......eeeeeeee.hhhhhhh.....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cg9 A  55 HMINKKSLLQNLLSKCKTTFQQSFTNANITLKDEKWLKNVRTAYFVCDHDGSVELAYLPNVLPKELVEEFTEKFESIQTGRKKDTGYSGILDNSMPFNYVTADLSQELGQYLSEIVNPQINYYISKLLTCVSSRTINYLVSLNDSYYALNNCLYPSTAFNSLKPSNDGHRIRKPHKDNLDITPSSLFYFGNFQNTEGYLELTDKNCKVFVQPGDVLFFKGNEYKHVVANITSGWRIGLVYFAHKGSKTKPYYEDTQKNSLKIHKETK 321
                                    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       


Chain B from PDB  Type:DNA  Length:11
                                           
                 5cg9 B   3 CATGCGCTGAC  13
                                    12 


Chain C from PDB  Type:DNA  Length:13
                                             
                 5cg9 C  14 TGTCAGxGCATGG  26
                                  | 23   
                                 20-5CM  


Chain D from PDB  Type:PROTEIN  Length:264
                                                                                                                                                                                                                                                                                                        
               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.hhhhhhh.eeeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5cg9 D  57 INKKSLLQNLLSKCKTTFQQSFTNANITLKDEKWLKNVRTAYFVCDHDGSVELAYLPNVLPKELVEEFTEKFESIQTGRKKDTGYSGILDNSMPFNYVTADLSQELGQYLSEIVNPQINYYISKLLTCVSSRTINYLVSLNDSYYALNNCLYPSTAFNSLKPSNDGHRIRKPHKDNLDITPSSLFYFGNFQNTEGYLELTDKNCKVFVQPGDVLFFKGNEYKHVVANITSGWRIGLVYFAHKGSKTKPYYEDTQKNSLKIHKET 320
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316    


Chain E from PDB  Type:DNA  Length:11
                                           
                 5cg9 E   3 CATGCGCTGAC  13
                                    12 


Chain F from PDB  Type:DNA  Length:13
                                             
                 5cg9 F  14 TGTCAGxGCATGG  26
                                  | 23   
                                 20-5CM
   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 5CG9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CG9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CG9)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)

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        D2W6T1_NAEGR | D2W6T1: 4lt5 5cg8

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5cg8