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(-) Description

Title :  CRYSTAL STRUCTURE OF M1.HPYAVI-SAM COMPLEX
 
Authors :  B. Ma, W. Liu, H. Zhang
Date :  07 Jan 16  (Deposition) - 16 Nov 16  (Release) - 30 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,E  (1x)
Biol. Unit 3:  D,H  (1x)
Biol. Unit 4:  F,G  (1x)
Keywords :  M1. Hpyavi, Sam, 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, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    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

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   C E   
Biological Unit 3 (1x):    D   H
Biological Unit 4 (1x):      FG 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1SAM8Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SAM2Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SAM2Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1SAM2Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1SAM2Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:8 , ALA A:9 , ASP A:29 , PRO A:30 , LYS A:165 , LYS A:167 , HIS A:168 , PRO A:194 , PHE A:195 , MET A:196 , GLY A:197 , SER A:198 , THR A:200 , GLU A:216 , SER A:217 , GLU A:218 , TYR A:221binding site for residue SAM A 301
2AC2SOFTWAREALA B:7 , ASP B:8 , ALA B:9 , ASP B:29 , PRO B:30 , HIS B:168 , THR B:170 , GLN B:171 , LYS B:172 , PRO B:194 , PHE B:195 , MET B:196 , GLY B:197 , SER B:198 , GLY B:199 , GLU B:216 , SER B:217 , TYR B:221binding site for residue SAM B 301
3AC3SOFTWAREASP C:8 , ALA C:9 , ASP C:29 , PRO C:31 , HIS C:168 , THR C:170 , GLN C:171 , LYS C:172 , PRO C:194 , PHE C:195 , MET C:196 , GLY C:197 , SER C:198 , GLY C:199 , THR C:200 , GLU C:216 , SER C:217 , GLU C:218 , TYR C:221binding site for residue SAM C 301
4AC4SOFTWAREALA D:7 , ASP D:8 , ALA D:9 , ASP D:29 , PRO D:31 , PHE D:195 , MET D:196 , GLY D:197 , SER D:198 , GLU D:216 , SER D:217 , GLU D:218 , TYR D:221binding site for residue SAM D 301
5AC5SOFTWAREASP E:8 , ALA E:9 , ASP E:29 , PRO E:169 , LYS E:172 , PHE E:195 , GLY E:197 , SER E:198 , GLY E:199 , THR E:200 , GLU E:216 , SER E:217binding site for residue SAM E 301
6AC6SOFTWAREASP F:8 , ALA F:9 , ASP F:29 , PRO F:31 , THR F:170 , GLN F:171 , LYS F:172 , PRO F:194 , PHE F:195 , MET F:196 , GLY F:197 , SER F:198 , GLU F:216 , SER F:217 , TYR F:221binding site for residue SAM F 301
7AC7SOFTWAREALA G:7 , ASP G:8 , ALA G:9 , ASP G:29 , HIS G:168 , THR G:170 , LYS G:172 , PHE G:195 , MET G:196 , GLY G:197 , SER G:198 , GLY G:199 , THR G:200 , GLU G:216 , SER G:217 , GLU G:218 , TYR G:221binding site for residue SAM G 301
8AC8SOFTWAREALA H:7 , ASP H:8 , ALA H:9 , ASP H:29 , PRO H:31 , THR H:170 , GLN H:171 , PRO H:194 , PHE H:195 , MET H:196 , GLY H:197 , SER H:198 , GLY H:199 , THR H:200 , GLU H:216 , SER H:217 , TYR H:221binding site for residue SAM H 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Met A:114 -Pro A:115
2Tyr A:149 -Leu A:150
3Lys B:61 -Leu B:62
4Met C:114 -Pro C:115
5His C:168 -Pro C:169
6His E:168 -Pro E:169
7Pro E:169 -Thr E:170
8Met F:114 -Pro F:115
9Phe G:60 -Lys G:61
10Met G:114 -Pro G:115
11Met H:114 -Pro H:115
12Ser H:157 -Pro H:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HFJ)

(-) 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:201
                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhh...eeeeee........hhhhhhhh..eeeeeeeeeee...hhhhhhhhhhhh.eeeeeeeeeee...............eeeeeeeee..................eee..............hhhhhhhhhhhh.....eee.....hhhhhhhhhh...eeeee.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hfj A   1 MIQIYHADAFEIIKDFYQQNLKVDAIITDPPYNFKLLEWIARYAPLVNPNGCMVIFCSYRFISYIADFLEENGFVVKDFIQWVKNNPMPRNIHRRYVQDTEFALWAVKKKAKWVFNKPKNEKYLRPLILKSPVVSGLEKTKHSLALMEKIISIHTNPNDIVLDPFMGSGTTGLACKNLERNFIGIESEKEYFQTAKKRLNL 231
                                    10        20        30 ||     66        76        86        96       106       116       126       136       146       156       166 ||    180       190       200       210       220       230 
                                                          32|                                                                                                          168|                                                          
                                                           59                                                                                                           173                                                          


Chain B from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhh...eeeeee.......hhhhhhhh..eeeeeeeeeee...hhhhhhhhhhhh.eeeeeeeeee................eeeeeeeee..............................hhhhhhhhhhhhh.....eee......hhhhhhhhh...eeeee.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hfj B   1 MIQIYHADAFEIIKDFYQQNLKVDAIITDPPNFKLLEWIARYAPLVNPNGCMVIFCSYRFISYIADFLEENGFVVKDFIQWVKNNPMPRNIHRRYVQDTEFALWAVKKKAKWVFNKPKNEKYLRPLILKKTKHPTQKSLALMEKIISIHTNPNDIVLDPFMGSGTTGLACKNLERNFIGIESEKEYFQTAKKRL 229
                                    10        20        30||      67        77        87        97       107       117       127       137       147       165       175       185       195       205       215       225    
                                                         31|                                                                                              156|                                                                
                                                          59                                                                                               165                                                                


Chain C from PDB  Type:PROTEIN  Length:204
                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhh...eeeeee......hhhhhhhhhhh..eeeeeeeeeee...hhhhhhhhhhhh.eeeeeeeeee................eeeeeeeee....................................hhhhhhhhhhhhh.....eee......hhhhhhhhh...eeeee.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5hfj C   1 MIQIYHADAFEIIKDFYQQNLKVDAIITDPPDKNFKLLEWIARYAPLVNPNGCMVIFCSYRFISYIADFLEENGFVVKDFIQWVKNNPMPRNIHRRYVQDTEFALWAVKKKAKWVFNKPKNEKYLRPLILKSPSGLEKTKHPTQKSLALMEKIISIHTNPNDIVLDPFMGSGTTGLACKNLERNFIGIESEKEYFQTAKKRLNL 231
                                    10        20        30||      65        75        85        95       105       115       125       135       145       155  ||   167       177       187       197       207       217       227    
                                                         31|                                                                                                  158|                                                                      
                                                          57                                                                                                   161                                                                      


Chain D from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhhhhhhhhh...eeeeee......hhhhhhhh..eeeeeeeeeee...hhhhhhhhhhhh.eeeeeeeeeee......hhhhh....eeeeeeeee...................ee...hhhhhhhhhhhh.....eee......hhhhhhhhh...eeeee.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hfj D   1 MIQIYHADAFEIIKDFYQQNLKVDAIITDPPFKLLEWIARYAPLVNPNGCMVIFCSYRFISYIADFLEENGFVVKDFIQWVKNNPMPRNIHRRYVQDTEFALWAVKKKAKWVFNKPKNEKYLRPLILKSSLALMEKIISIHTNPNDIVLDPFMGSGTTGLACKNLERNFIGIESEKEYFQTAKKRLNL 231
                                    10        20        30||      68        78        88        98       108       118       128       138       148       173       183       193       203       213       223        
                                                         31|                                                                                              157|                                                          
                                                          60                                                                                               173                                                          


Chain E from PDB  Type:PROTEIN  Length:193
                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhhhhhhhhh...eeeeee....hhhhhhhhhhh..eeeeeeeeeee...hhhhhhhhhhhh.eeeeeeeeeee...............eeeeeeeee...................ee.......hhhhhhhhhhhhh.....eee......hhhhhhhhh...eeeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hfj E   1 MIQIYHADAFEIIKDFYQQNLKVDAIITDPPNFKLLEWIARYAPLVNPNGCMVIFCSYRFISYIADFLEENGFVVKDFIQWVKNNPMPRNIHRRYVQDTEFALWAVKKKAKWVFNKPKNEKYLRPLILKSHPTQKSLALMEKIISIHTNPNDIVLDPFMGSGTTGLACKNLERNFIGIESEKEYFQTAKKRLN 230
                                    10        20        30||      67        77        87        97       107       117       127       137       147       157|      177       187       197       207       217       227   
                                                         31|                                                                                               157|                                                              
                                                          59                                                                                                168                                                              


Chain F from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhh...eeeeee....hhhhhhhhhhh..eeeeeeeeeee...hhhhhhhhhhhh.eeeeeeeeee................eeeeeeeee............................hhhhhhhhhhhhh.....eee......hhhhhhhhh...eeeee.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hfj F   1 MIQIYHADAFEIIKDFYQQNLKVDAIITDPPNFKLLEWIARYAPLVNPNGCMVIFCSYRFISYIADFLEENGFVVKDFIQWVKNNPMPRNIHRRYVQDTEFALWAVKKKAKWVFNKPKNEKYLRPLILKSPPTQKSLALMEKIISIHTNPNDIVLDPFMGSGTTGLACKNLERNFIGIESEKEYFQTAKKRLNL 231
                                    10        20        30||      67        77        87        97       107       117       127       137       147       157||     177       187       197       207       217       227    
                                                         31|                                                                                                158|                                                              
                                                          59                                                                                                 169                                                              


Chain G from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               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.......hhhhhhhh...eeeee.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hfj G   1 MIQIYHADAFEIIKDFYQQNLKVDAIITDPPYDKNFKLLEWIARYAPLVNPNGCMVIFCSYRFISYIADFLEENGFVVKDFIQWVKNNPMPRNIHRRYVQDTEFALWAVKKKAKWVFNKPKNEKYLRPLILKSPEKTKHPTQKSLALMEKIISIHTNPNDIVLDPFMGSGTTGLACKNLERNFIGIESEKEYFQTAKKRL 229
                                    10        20        30 ||     64        74        84        94       104       114       124       134       144       154   ||  169       179       189       199       209       219       229
                                                          32|                                                                                                  158|                                                                 
                                                           57                                                                                                   164                                                                 


Chain H from PDB  Type:PROTEIN  Length:193
                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhh...eeeeee....hhhhhhhhhhh..eeeeeeeeee....hhhhhhhhhhhh.eeeeeeeeeee...............eeeeeeeee..................eee.......hhhhhhhhhhhhh.....eee......hhhhhhhhh...eeeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hfj H   1 MIQIYHADAFEIIKDFYQQNLKVDAIITDPPNFKLLEWIARYAPLVNPNGCMVIFCSYRFISYIADFLEENGFVVKDFIQWVKNNPMPRNIHRRYVQDTEFALWAVKKKAKWVFNKPKNEKYLRPLILKSPPTQKSLALMEKIISIHTNPNDIVLDPFMGSGTTGLACKNLERNFIGIESEKEYFQTAKKRLN 230
                                    10        20        30||      67        77        87        97       107       117       127       137       147       157||     177       187       197       207       217       227   
                                                         31|                                                                                                158|                                                             
                                                          59                                                                                                 169
   Legend:   → Mismatch (orange background)
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  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 5HFJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

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5hek