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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ALKBH5 CRYSTALLIZED IN THE PRESENCE OF MN^{2+} AND 2-OXOGLUTARATE
 
Authors :  W. Tempel, X. Chao, K. Liu, A. Dong, T. Cerovina, H. He, C. Bountra, C. H. Arrowsmith, A. M. Edwards, J. Min, Structural Genomics Consor (Sgc)
Date :  09 Jan 14  (Deposition) - 16 Apr 14  (Release) - 24 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Structural Genomics Consortium, Sgc, Rna Demethylase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Xu, K. Liu, W. Tempel, M. Demetriades, W. Aik, C. J. Schofield, J. Min
Structures Of Human Alkbh5 Demethylase Reveal A Unique Binding Mode For Specific Single-Stranded N6-Methyladenosin Rna Demethylation.
J. Biol. Chem. V. 289 17299 2014
PubMed-ID: 24778178  |  Reference-DOI: 10.1074/JBC.M114.550350

(-) Compounds

Molecule 1 - RNA DEMETHYLASE ALKBH5
    ChainsA, B
    EC Number1.14.11.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28-MHL
    Expression System StrainBL21-V2R-PRARE2
    Expression System Taxid562
    FragmentUNP RESIDUES 74-294
    GeneALKBH5, ABH5, OFOXD1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymALKYLATED DNA REPAIR PROTEIN ALKB HOMOLOG 5, ALPHA- KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB HOMOLOG 5

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 27)

Asymmetric Unit (3, 27)
No.NameCountTypeFull Name
1AKG2Ligand/Ion2-OXOGLUTARIC ACID
2MN2Ligand/IonMANGANESE (II) ION
3UNX23Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1AKG1Ligand/Ion2-OXOGLUTARIC ACID
2MN-1Ligand/IonMANGANESE (II) ION
3UNX9Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 2 (2, 15)
No.NameCountTypeFull Name
1AKG1Ligand/Ion2-OXOGLUTARIC ACID
2MN-1Ligand/IonMANGANESE (II) ION
3UNX14Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:204 , ASP A:206 , HIS A:266 , AKG A:502BINDING SITE FOR RESIDUE MN A 501
2AC2SOFTWAREASN A:193 , TYR A:195 , HIS A:204 , ASP A:206 , HIS A:266 , ILE A:268 , ARG A:277 , VAL A:279 , ILE A:281 , MN A:501BINDING SITE FOR RESIDUE AKG A 502
3AC3SOFTWAREHIS B:204 , ASP B:206 , HIS B:266 , AKG B:502BINDING SITE FOR RESIDUE MN B 501
4AC4SOFTWAREASN B:193 , TYR B:195 , HIS B:204 , ASP B:206 , HIS B:266 , ILE B:268 , ARG B:277 , VAL B:279 , ILE B:281 , ARG B:283 , MN B:501BINDING SITE FOR RESIDUE AKG B 502

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:230 -A:267
2B:230 -B:267

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg A:213 -Pro A:214
2Arg B:213 -Pro B:214

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OCT)

(-) 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:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhheeeee..hhhhhhhhhhhhhhhhhhhhh...hhh.eeee..eeeeee......................hhhhhhhhhhhhhhh.........eeeeeee.....eeee..........eeeeee...eeeee.hhhhh.........eeeee...eeeee.hhhhhh..eeehhhhh...eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4oct A  77 QKEEEARKVKSGIRQMRLFSQDECAKIEARIDEVVSRAEKGLYNEHTVDRAPLRNKYFFGEGYTRGPGQERLYPPGDVDEIPEWVHQLVIQKLVEHRVIPEGFVNSAVINDYQPGGCIVSHVDPIHIFERPIVSVSFFSDSALCFGCKFQFKPIRVSEPVLSLPVRRGSVTVLSGYAADEITHCIRPQDIKERRAVIILRKTRLDAPRLE 293
                                    86        96       106       116       126       136   ||  153       163       173       183       193       203       213       223       233       243       253       263       273       283       293
                                                                                         140|                                                                                                                                                 
                                                                                          148                                                                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhheeeee..hhhhhhhhhhhhhhhhhhhhh...hhh.eeee..eeeeee.....................hhhhhhhhhhhhhhh.........eeeeeee.....eeee..........eeeeee...eeeee.hhhhh.........eeeee...eeeee.hhhhhh..eeehhhhh...eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4oct B  76 LQKEEEARKVKSGIRQMRLFSQDECAKIEARIDEVVSRAEKGLYNEHTVDRAPLRNKYFFGEGYTGPGQERLYPPGDVDEIPEWVHQLVIQKLVEHRVIPEGFVNSAVINDYQPGGCIVSHVDPIHIFERPIVSVSFFSDSALCFGCKFQFKPIRVSEPVLSLPVRRGSVTVLSGYAADEITHCIRPQDIKERRAVIILRKTRLDAPRLE 293
                                    85        95       105       115       125       135    || 153       163       173       183       193       203       213       223       233       243       253       263       273       283       293
                                                                                          140|                                                                                                                                                
                                                                                           149                                                                                                                                                

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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 4OCT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        ALKB5_HUMAN | Q6P6C24nj4 4nrm 4nro 4nrp 4nrq 4o61 4o7x

(-) Related Entries Specified in the PDB File

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