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(-) Description

Title :  CRYSTAL STRUCTURE OF ALKB D135I MUTANT PROTEIN WITH COFACTORS BOUND TO DSDNA CONTAINING M6A/A
 
Authors :  C. Q. Yi, C. X. Zhu
Date :  06 Nov 13  (Deposition) - 16 Apr 14  (Release) - 28 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.62
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dna/Rna Direct Repair, Jelly-Roll Fold, Dna/Rna Demethylation Repair, Fe(Ii), 2-Kg, Oxidoreductase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Zhu, C. Yi
Switching Demethylation Activities Between Alkb Family Rna/Dna Demethylases Through Exchange Of Active-Site Residues.
Angew. Chem. Int. Ed. Engl. V. 53 3659 2014
PubMed-ID: 24596302  |  Reference-DOI: 10.1002/ANIE.201310050

(-) Compounds

Molecule 1 - ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB
    Chains: A
    EC Number: 1.14.11.33
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 12-215
    Gene: ALKB, AIDD, B2212, JW2200
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: ALKYLATED DNA REPAIR PROTEIN ALKB, DNA OXIDATIVE DEMETHYLASE ALKB
 
Molecule 2 - 5'-D(*TP*AP*GP*GP*TP*AP*AP*(6MA)P*AP*CP*CP*GP*T)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3'
    Chains: 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, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
12YR1Mod. Nucleotide2'-DEOXY-N-(2-SULFANYLETHYL)CYTIDINE 5'-(DIHYDROGENPHOSPHATE)
26MA1Mod. NucleotideN6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE
3AKG1Ligand/Ion2-OXOGLUTARIC ACID
4MN1Ligand/IonMANGANESE (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:131 , ASP A:133 , HIS A:187 , AKG A:302 , HOH A:449BINDING SITE FOR RESIDUE MN A 301
2AC2SOFTWARELEU A:118 , ASN A:120 , TYR A:122 , LEU A:128 , HIS A:131 , ASP A:133 , HIS A:187 , ILE A:189 , ARG A:204 , ASN A:206 , THR A:208 , MN A:301 , HOH A:409 , HOH A:415 , HOH A:449 , HOH A:452 , 6MA B:8BINDING SITE FOR RESIDUE AKG A 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NII)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NII)

(-) 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:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeee......hhhhhhhhhhhhhhhh...............eeeee...eeeee..eeeee.ee....ee....hhhhhhhhhhhhhhh........eeeeeee.....eeee........eeeeeee..eeeee.........eeeee....eeeehhhhh...eee..............eeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nii A  12 QEPLAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAMTNCGHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAKLCLHQDKILRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQAGK 214
                                    21        31        41        51        61        71        81        91       101       111       121       131   ||  144       154       164       174       184       194       204       214
                                                                                                                                                     135|                                                                           
                                                                                                                                                      139                                                                           


Chain B from PDB  Type:DNA  Length:12
                                            
                 4nii B   2 AGGTAAaAxCGT  13
                                  | 11  
                                  8-6MA 
                                   10-2YR


Chain C from PDB  Type:DNA  Length:13
                                             
                 4nii C   1 AACGGTATTACCT  13
                                    10
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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 4NII)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

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  4nii
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  ALKB_ECOLI | P05050
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 Related Entries

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

UniProtKB/Swiss-Prot
        ALKB_ECOLI | P05050: 2fd8 2fdf 2fdg 2fdh 2fdi 2fdj 2fdk 3bi3 3bie 3bkz 3i2o 3i3m 3i3q 3i49 3khb 3khc 3o1m 3o1o 3o1p 3o1r 3o1s 3o1t 3o1u 3o1v 3t3y 3t4h 3t4v 4jht 4nid 4nig 4nih 4rfr 4zhn

(-) Related Entries Specified in the PDB File

4nid 4nig 4nih