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(-) Description

Title :  STRUCTURAL BASIS OF ASYMMETRIC DNA METHYLATION AND ATP-TRIGGERED LONG-RANGE DIFFUSION BY ECOP15I
 
Authors :  Y. K. Gupta, S. H. Chan, S. Y. Xu, A. K. Aggarwal
Date :  15 Apr 15  (Deposition) - 29 Jul 15  (Release) - 29 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Hydrolase/Dna, Atp Motor, Dna Methyltransferase, Asymmetric Dna Methylation, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. K. Gupta, S. H. Chan, S. Y. Xu, A. K. Aggarwal
Structural Basis Of Asymmetric Dna Methylation And Atp-Triggered Long-Range Diffusion By Ecop15I.
Nat Commun V. 6 7363 2015
PubMed-ID: 26067164  |  Reference-DOI: 10.1038/NCOMMS8363

(-) Compounds

Molecule 1 - RESTRICTION ENDONUCLEASE ECOP15I, MODIFICATION SUBUNIT
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: NEB EXPRESS
    Expression System Taxid: 562
    Gene: ECOP15IMOD
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - RESTRICTION ENDONUCLEASE ECOP15I, RESTRICTION SUBUNIT
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: NEB EXPRESS
    Expression System Taxid: 562
    Gene: ECOP15IRES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 3 - DNA 20-MER ATACAGCAGTAGACTATGAT
    Chains: D
    Engineered: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synthetic: YES
 
Molecule 4 - DNA 20-MER AATCATAGTCTACTGCTGTA
    Chains: E
    Engineered: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2CA1Ligand/IonCALCIUM ION
3MN2Ligand/IonMANGANESE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:201binding site for residue MN A 701
2AC2SOFTWAREGLU A:213 , HIS C:168binding site for residue MN A 702
3AC3SOFTWAREGLN C:14 , GLY C:89 , LYS C:90 , THR C:91 , TYR C:92 , ILE C:119 , GLY C:122 , THR C:123 , PHE C:126 , ASP C:226 , GLU C:227 , ASP C:509 , ARG C:537binding site for residue AMP C 1001
4AC4SOFTWAREHOH B:717 , HOH B:723 , DA D:8 , HOH D:202binding site for residue CA D 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Trp A:301 -Pro A:302
2Ile B:6 -Phe B:7
3Trp B:301 -Pro B:302
4Gly B:568 -Tyr B:569
5Tyr B:569 -Lys B:570
6Lys B:601 -Asp B:602
7Asn B:632 -Lys B:633
8Lys B:633 -Lys B:634
9Lys C:9 -Asn C:10

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZCF)

(-) 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:616
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh......hhhhhhhhhh.......eeee.hhhhhhhhhhh...eeeeehhhhhhh........eeee.hhhhhhhhhhhhhh..eeeeee..................hhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhheeeeeeeeeee...hhhhhhhhhhhhhh...eeeeeeee.........ee..eeeeeeee..............hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.......eee..eeeeee.................................hhhhhhhhhhh..ee.........eeeee.hhh...ee.eee.hhhhhhhhhhh...........hhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhh....eeeeeeee.........hhhhh..hhhhhhhhhhhhhhhh......eeeeeee..................hhhhhhhhhhhhhhhh........eeeee..eeeeee..eeee.....hhhhhhhhhhhhhh.......eeeee.hhh.hhhhhhhhhhhhh......eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zcf A  13 ANSKQLAVLKANFPQCFDKNGAFIQEKLLEIIRASEKESYSLNWLGKSYARLLANLPPKTLLAEDKTHNQQEENKNSQHLLIKGDNLEVLKHMVNAYAEKVKMIYIDPPYNTGKDGFVYNDDRFTPEQLSELAGIDLDEAKRILEFTTKGSSSHSAWLTFIYPRLYIARELMREDGTIFISIDHNEFSQLKLVCDEIFGEQNHVGDLVWKNATDNNPSNIAVEHEYIIVYTKNKEQLISEWKSNISDVKNLLVNIGEEFASKYTGNELQEKYTQWFREHRSELWPLDRYKYIDKDGIYTGSQSVHNPGKEGYRYDIIHPKTKKPCKQPLMGYRFPLDTMDRLLSEEKIIFGDDENKIIELKVYAKDYKQKLSSVIHLDGRVATNELKELFPMTQPFNAKTIKLVEDLISFACDGEGIVLDFFAGSGTTAHTVFNLNNKNKTSYQFITVQLDEPTKKSDAMKHGYNTIFDLTKERLIRASKKNRDQGFKVYQLMPDFRAKDESELTFFDDVVLTPEQYDTLLTTWCLYDGSLLTTPIEDVDLGGYKAHLCDGRLYLIAPNFTSEALKALLQKVDSDKDFAPNKVVFYGSNFSAKQMELNEALKSYANSIELDLVVRN 644
                                    22        32        42     || 56        66        76        86        96       106       116       126       136  ||   147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407||   ||419       429       439       449       459       469    || 480       490       500       510       520   ||  535       545       555       565       575       585       595       605       615|      626     ||638      
                                                              48|                                                                                   139|                                                                                                                                                                                                                                                                        408| 414|                                                       474|                                             524|                                                                                  615|            632|         
                                                               53                                                                                    141                                                                                                                                                                                                                                                                         410  416                                                        476                                              530                                                                                   617             635         


Chain B from PDB  Type:PROTEIN  Length:612
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee........hhhhhhhhhhhhhhhh.....hhhhhhhhhhhh........eeee..hhhhhhhhhhh....eeee..hhhhh........eeee.hhhhhhhhhhhhhh..eeeeee...................hhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhheeeeeeeeeee...hhhhhhhhhhhhhh...eeeeeeee.........ee..eeeeeeee.............hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.......eee..eeeeee.................................hhhhhhhhhhh..ee........eeeee.hhh...ee.eee...hhhhhhhhhhh...........hhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhh..eeeeeeee........hhhhhh...hhhhhhhhhhhhhhhh......eeeeee......hhhhhhhhhhhhhhhh........eee......eeee..eeee.......hhhhhh........eeeee....hhhhhhhhhhhhhh.......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4zcf B   2 KKETIFEVETANSKQLAVLKANFPQCFDNGAFIQEKLLEIIRASEVELSKESYSLNWLGKSYARLLANLPPKTLLAEDKTHNQQEENKNSQHLLIKGDNLEVLKHMVNAYAEKVKMIYIDPPYNTGKDGFVYNDDRKFTPEQLSELAGIDLDEAKRILEFTTKGSSSHSAWLTFIYPRLYIARELMREDGTIFISIDHNEFSQLKLVCDEIFGEQNHVGDLVWKNATDNNPSNIAVEHEYIIVYTKKEQLISEWKSNISDVKNLLVNIGEEFASKYTGNELQEKYTQWFREHRSELWPLDRYKYIDKDGIYTGSQSVHNPGKEGYRYDIIHPKTKKPCKQPLMGYRFPLDTMDRLLSEEKIIFGDDEKIIELKVYAKDYKQKLSSVIHLDGRVATNELKELFPEMTQPFTNAKTIKLVEDLISFACDGEGIVLDFFAGSGTTAHTVFNLNNKNKTSYQFITVQLDEPTKDKSDAMKHGYNTIFDLTKERLIRASKKNRDQGFKVYQLMPDFVVLTPEQYDTLLTTWCLYDGSLLTTPIEDVDLGGYKAHLCDGRLYLIAPNFTALKALLQKDKDFAPNKVVFYGSNSAKQMELNEALKSYANKKELDLVVRN 644
                                 || 12        22       |33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243     ||254       264       274       284       294       304       314       324       334       344       354       364      |375       385       395       405       415       425       435       445       455       465       475       485       495       505       515||     543       553       563       573       583  ||   595||     608     ||620       630   ||  642  
                                 7|                   30|                                                                                                                                                                                                                      249|                                                                                                                     371|                                                                                                                                            516|                                                586|    596|           614|              634|       
                                  9                    32                                                                                                                                                                                                                       251                                                                                                                      373                                                                                                                                             535                                                 589     600            617               637       


Chain C from PDB  Type:PROTEIN  Length:627
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh..eee...hhhhhhhh..eee.hhhhhhhhhhhhhhhhh.............eeeeee....hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee......hhhhhhhhhh.....eeeeeeehhhhhhhhhhh.............hhhhhhhh...eeeee.hhhh...hhhhhhhhh.....eeeee.........eeeeehhhhhhhh....eeeeee....eeee...eeeee..eee..............eee...eee....ee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee...hhhhhhhhhhhhhhh..hhhhhhhhhhhh...ee..hhhhhhhhhhhhhhh.......eeeee.hhhhhh....eeeeee....hhhhhhhhh..............eeeeee.....hhhhhhhhhhhhhh........eee..hhhhhhhhhhhhh..hhhhhhhh..ee......hhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.....ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zcf C   6 TLEKNLPHQKAGVDAVMNVFVSATPHLTDNVAVRLLANPELKLSEQQYYNNIKNVQAFNGIAHSKDNHNAKSNIIDVSMETGTGKTYTYIKTIFDLNKSFGINKFIIIVPTLSIKAGTVNFLKSDALKEHFRDDYKRELRTYVVESQKMPQAIHDFVEASNFKKYIHVLVINSGMINSKSLTDTYDTGLLDNQFNTPVDALRAVKPFIIIDEPHRFPTGKKTWENIEKFNAQYIIRYGATFSEGYKNLVYRLTAVDAFNDDLVKGIDAYIEDNANLKFVKDGKEATFFKLAKSLSKTHSAIHDLTLDALNTAVLSNGIELKIGSSINPYSYDQTLADNMMRKAVKEHFKLEKELLTQPRIKPLTLFFIDDLKTKFEEYVLAEANELLYKNYLEKTVTNISSVHGGYIEQEINEILHDKELLLSLDNPRRFIFSKWTLREGWDNPNVFQICKLRSSKLQEVGRGLRLPVNEYMCRVKNFTLKYYVDFTEKDFVDSLVKEVNESSPSKFTQELKEQIDNFKDSDAYSRLKSELKELWDLINQKAVIEYKINSESEFLSIFKSFMLEETERSYREFLDNLSQTIFVKHGTLHKVFCDIKDTILNIQTIRKIKSGFSKYLLNNSFSLGYNL 810
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       164       174 ||    185       195       205       215       225       235       245       255       265       275       285 ||    300|     |321 ||    333       343|      355       365       375       385      |396       406|      429      |446       456     ||477       487       497       507       517   ||  532       542     ||554       564       574  ||   589    || 624       667       677       687       697       745       755       765       780       790       800|      
                                                                                                                                                                             153|          176|                                                                                                          287|    300|   308| 323|              343|                                           392|         406|             436|               462|                                            521|                  548|                       577|        594|          633|                                   705|                           774|                 800|      
                                                                                                                                                                              163           178                                                                                                           293     302    319  326               346                                            394          420              444                474                                             527                   551                        583         620           667                                    744                            780                  804      


Chain D from PDB  Type:DNA  Length:20
                                                    
                 4zcf D   1 ATACAGCAGTAGACTATGAT  20
                                    10        20


Chain E from PDB  Type:DNA  Length:20
                                                    
                 4zcf E   1 AATCATAGTCTACTGCTGTA  20
                                    10        20
   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 4ZCF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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  4zcf
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 Related Entries

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