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(-) Description

Title :  CRYSTAL STRUCTURE OF M1.HPYAVI
 
Authors :  B. Ma, H. Zhang, W. Liu
Date :  06 Jan 16  (Deposition) - 16 Nov 16  (Release) - 30 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,C  (1x)
Biol. Unit 3:  B,D  (1x)
Keywords :  M1. Hpyavi, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Ma, J. Ma, D. Liu, L. Guo, H. Chen, J. Ding, W. Liu, H. Zhang
Biochemical And Structural Characterization Of A Dna N6-Adenine Methyltransferase From Helicobacter Pylori
Oncotarget V. 7 40965 2016
PubMed-ID: 27259995  |  Reference-DOI: 10.18632/ONCOTARGET.9692

(-) Compounds

Molecule 1 - ADENINE SPECIFIC DNA METHYLTRANSFERASE (DPNA)
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: HP_0050
    Organism Scientific: HELICOBACTER PYLORI (STRAIN ATCC 700392 / 26695)
    Organism Taxid: 85962
    Strain: ATCC 700392 / 26695

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (1x): A C 
Biological Unit 3 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5HEK)

(-) Sites  (0, 0)

(no "Site" information available for 5HEK)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Lys A:61 -Leu A:62
2Met A:114 -Pro A:115
3Pro A:115 -Arg A:116
4Asn A:146 -Glu A:147
5Gln A:171 -Lys A:172
6Asn B:117 -Ile B:118
7Val D:109 -Lys D:110
8Asn D:230 -Leu D:231

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HEK)

(-) 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:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhh...eeeeee..........hhhhhhhh..eeeeeeeeeee...hhhhhhhhhh...eeeeeeeeee................eeeeeeeee...........................hhhhhhhhhhhhh.....eee......hhhhhhhhh...eeeee.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hek A   1 MIQIYHADAFEIIKDFYQQNLKVDAIITDPPYNKNFKLLEWIARYAPLVNPNGCMVIFCSYRFISYIADFLEENGFVVKDFIQWVKNNPMPRNIHRRYVQDTEFALWAVKKKAKWVFNKPKNEKYLRPLILKSPVQKSLALMEKIISIHTNPNDIVLDPFMGSGTTGLACKNLERNFIGIESEKEYFQTAKKRLNLF 232
                                    10        20        30  ||    64        74        84        94       104       114       124       134       144       154    || 175       185       195       205       215       225       
                                                           33|                                                                                                  159|                                                             
                                                            58                                                                                                   171                                                             


Chain B from PDB  Type:PROTEIN  Length:185
                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhh...eeeeee....hhhhhhhhhhh..eeeeeeeeeee...hhhhhhhhhhhh.eeeeeeeeee...............eeeeeeeee.....................hhhhhhhhhhhh.....eee......hhhhhhhhh...eeeee.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hek B   1 MIQIYHADAFEIIKDFYQQNLKVDAIITDPPNFKLLEWIARYAPLVNPNGCMVIFCSYRFISYIADFLEENGFVVKDFIQWVKNNPMPNIHRRYVQDTEFALWAVKKKAKWVFNKPKNEKYLRPLLSLALMEKIISIHTNPNDIVLDPFMGSGTTGLACKNLERNFIGIESEKEYFQTAKKRLNL 231
                                    10        20        30||      67        77        87        97       107       118       128       138       148    |||176       186       196       206       216       226     
                                                         31|                                                     115|                                 153||                                                          
                                                          59                                                      117                                  155|                                                          
                                                                                                                                                        173                                                          


Chain C from PDB  Type:PROTEIN  Length:185
                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhhhhhhhhh...eeeeee....hhhhhhhh..eeeeeeeeeee...hhhhhhhhhhhh.eeeeeeeeee...............eeeeeeeee.......................hhhhhhhhhhhhh.....eee......hhhhhhhhh...eeeee.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hek C   1 MIQIYHADAFEIIKDFYQQNLKVDAIITDPPLLEWIARYAPLVNPNGCMVIFCSYRFISYIADFLEENGFVVKDFIQWVKNNPPRNIHRRYVQDTEFALWAVKKKAKWVFNKPKNEKYLRPLILKKSLALMEKIISIHTNPNDIVLDPFMGSGTTGLACKNLERNFIGIESEKEYFQTAKKRLNL 231
                                    10        20        30||      70        80        90       100       110  ||   121       131       141       151    || 176       186       196       206       216       226     
                                                         31|                                                113|                                      156|                                                           
                                                          62                                                 115                                       172                                                           


Chain D from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhh...eeeeee.....hhhhhhhh..eeeeeeeeeee...hhhhhhhhhhhh.eeeeeeeee...........eeeeeeee....................hhhhhhhhhhhhh.....eee......hhhhhhhhh...eeeee.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hek D   1 MIQIYHADAFEIIKDFYQQNLKVDAIITDPPKLLEWIARYAPLVNPNGCMVIFCSYRFISYIADFLEENGFVVKDFIQWVKIHRRYVQDTEFALWAVKKKAKWVFNKPKNKLRPLILKSLALMEKIISIHTNPNDIVLDPFMGSGTTGLACKNLERNFIGIESEKEYFQTAKKRLNL 231
                                    10        20        30||      69        79        89        99       109||     126       136       146||    |174       184       194       204       214       224       
                                                         31|                                              110|                         146||  155|                                                           
                                                          61                                               118                          148|   172                                                           
                                                                                                                                         150
   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 5HEK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn A:146 - Glu A:147   [ RasMol ]  
    Asn B:117 - Ile B:118   [ RasMol ]  
    Asn D:230 - Leu D:231   [ RasMol ]  
    Gln A:171 - Lys A:172   [ RasMol ]  
    Lys A:61 - Leu A:62   [ RasMol ]  
    Met A:114 - Pro A:115   [ RasMol ]  
    Pro A:115 - Arg A:116   [ RasMol ]  
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        O24891_HELPY | O24891: 5hfj

(-) Related Entries Specified in the PDB File

5hfj