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(-) Description

Title :  THREE-DIMENSIONAL STRUCTURE OF DNA SEQUENCE SPECIFICITY (S) SUBUNIT OF A TYPE I RESTRICTION-MODIFICATION ENZYME AND ITS FUNCTIONAL IMPLICATIONS
 
Authors :  J. S. Kim, A. Degiovanni, J. Jancarik, P. D. Adams, H. A. Yokota, R. Kim, S Berkeley Structural Genomics Center (Bsgc)
Date :  30 Dec 04  (Deposition) - 15 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Type I Restriction Modification Enzyme, S-Subunit, Structural Genomics, Psi, Protein Structure Initiative, Berkeley Structural Genomics Center, Bsgc, Hydrolase Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. S. Kim, A. Degiovanni, J. Jancarik, P. D. Adams, H. Yokota, R. Kim, S. H. Kim
Crystal Structure Of Dna Sequence Specificity Subunit Of A Type I Restriction-Modification Enzyme And Its Functional Implications.
Proc. Natl. Acad. Sci. Usa V. 102 3248 2005
PubMed-ID: 15728358  |  Reference-DOI: 10.1073/PNAS.0409851102

(-) Compounds

Molecule 1 - TYPE I RESTRICTION-MODIFICATION ENZYME, S SUBUNIT
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PB3
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 243232
    Strain: DSM 2661

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1YF2)

(-) Sites  (0, 0)

(no "Site" information available for 1YF2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YF2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YF2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YF2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YF2)

(-) Exons   (0, 0)

(no "Exon" information available for 1YF2)

(-) 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:425
 aligned with T1S1_METJA | Q57594 from UniProtKB/Swiss-Prot  Length:425

    Alignment length:425
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420     
           T1S1_METJA     1 MFYKEENFKKTEIGEIPEDWEIVELKDVCKKIKAGGTPKTSVEEYYKNGTIPFVKIEDITNSNKYLTNTKIKITEEGLNNSNAWIVPKNSVLFAMYGSIGETAINKIEVATNQAILGIIPKDNILESEFLYYILAKNKNYYSKLGMQTTQKNLNAQIVKSFKIPLPPLEEQKQIAKILTKIDEGIEIIEKSINKLERIKKGLMHKLLTKGIGHSRFKKSEIGEIPEDWEVFEIKDIFEVKTGTTPSTKKSEYWENGEINWITPLDLSRLNEKIYIGSSERKVTKIALEKCNLNLIPKGSIIISTRAPVGYVAVLTVESTFNQGCKGLFQKNNDSVNTEFYAYYLKFKKNLLENLSGGSTFKELSKSMLENFKIPLPPLEEQKQIAKILSSVDKSIELKKQKKEKLQRMKKKIMELLLTGKVRVKT 425
               SCOP domains d1yf2a1 A:1-220 Bipartite methylase S protein MJ0130                                                                                                                                                                        d1yf2a2 A:221-425 Bipartite methylase S protein MJ0130                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................eehhhheeeeee.......hhhhh....eeeehhhhhhh...ee....eeehhhhhhh..........eeee.......eeee....ee...eeeeee.....hhhhhhhhhhhhhhhhhh..........hhhhhhh.ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee......ee...eeeehhhheeeee.......hhhhh....eeeehhhhhhh.....ee.....eehhhhhhhh.........eeee.......eeee....ee...eeeeee......hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhheeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yf2 A   1 MFYKEENFKKTEIGEIPEDWEIVELKDVCKKIKAGGTPKTSVEEYYKNGTIPFVKIEDITNSNKYLTNTKIKITEEGLNNSNAWIVPKNSVLFAMYGSIGETAINKIEVATNQAILGIIPKDNILESEFLYYILAKNKNYYSKLGMQTTQKNLNAQIVKSFKIPLPPLEEQKQIAKILTKIDEGIEIIEKSINKLERIKKGLMHKLLTKGIGHSRFKKSEIGEIPEDWEVFEIKDIFEVKTGTTPSTKKSEYWENGEINWITPLDLSRLNEKIYIGSSERKVTKIALEKCNLNLIPKGSIIISTRAPVGYVAVLTVESTFNQGCKGLFQKNNDSVNTEFYAYYLKFKKNLLENLSGGSTFKELSKSMLENFKIPLPPLEEQKQIAKILSSVDKSIELKKQKKEKLQRMKKKIMELLLTGKVRVKT 425
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420     


Chain B from PDB  Type:PROTEIN  Length:425
 aligned with T1S1_METJA | Q57594 from UniProtKB/Swiss-Prot  Length:425

    Alignment length:425
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420     
           T1S1_METJA     1 MFYKEENFKKTEIGEIPEDWEIVELKDVCKKIKAGGTPKTSVEEYYKNGTIPFVKIEDITNSNKYLTNTKIKITEEGLNNSNAWIVPKNSVLFAMYGSIGETAINKIEVATNQAILGIIPKDNILESEFLYYILAKNKNYYSKLGMQTTQKNLNAQIVKSFKIPLPPLEEQKQIAKILTKIDEGIEIIEKSINKLERIKKGLMHKLLTKGIGHSRFKKSEIGEIPEDWEVFEIKDIFEVKTGTTPSTKKSEYWENGEINWITPLDLSRLNEKIYIGSSERKVTKIALEKCNLNLIPKGSIIISTRAPVGYVAVLTVESTFNQGCKGLFQKNNDSVNTEFYAYYLKFKKNLLENLSGGSTFKELSKSMLENFKIPLPPLEEQKQIAKILSSVDKSIELKKQKKEKLQRMKKKIMELLLTGKVRVKT 425
               SCOP domains d1yf2b1 B:1-220 Bipartite methylase S protein MJ0130                                                                                                                                                                        d1yf2b2 B:221-425 Bipartite methylase S protein MJ0130                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Methylase_S-1yf2B01 B:225-407                                                                                                                                                          ------------------ Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Methylase_S-1yf2B02 B:225-407                                                                                                                                                          ------------------ Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Methylase_S-1yf2B03 B:225-407                                                                                                                                                          ------------------ Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Methylase_S-1yf2B04 B:225-407                                                                                                                                                          ------------------ Pfam domains (4)
         Sec.struct. author ..eee...ee.....ee....eeehhhheeeeee.......hhhhh....eeeehhhhhhhh..ee....eeehhhhhhh..........eeee.......eeee....ee...eeeeee.....hhhhhhhhhhhhhhhhhhhhhh......hhhhhh..eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee..eeee...eeeehhhheeee........hhhhh....eeeehhhhhh......ee.....eehhhhhh...........eeee.......eeee....ee...eeeeee......hhhhhhhhhhhhhhhhhhhhh.......hhhhhhh.eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yf2 B   1 MFYKEENFKKTEIGEIPEDWEIVELKDVCKKIKAGGTPKTSVEEYYKNGTIPFVKIEDITNSNKYLTNTKIKITEEGLNNSNAWIVPKNSVLFAMYGSIGETAINKIEVATNQAILGIIPKDNILESEFLYYILAKNKNYYSKLGMQTTQKNLNAQIVKSFKIPLPPLEEQKQIAKILTKIDEGIEIIEKSINKLERIKKGLMHKLLTKGIGHSRFKKSEIGEIPEDWEVFEIKDIFEVKTGTTPSTKKSEYWENGEINWITPLDLSRLNEKIYIGSSERKVTKIALEKCNLNLIPKGSIIISTRAPVGYVAVLTVESTFNQGCKGLFQKNNDSVNTEFYAYYLKFKKNLLENLSGGSTFKELSKSMLENFKIPLPPLEEQKQIAKILSSVDKSIELKKQKKEKLQRMKKKIMELLLTGKVRVKT 425
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420
   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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YF2)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: TRD (7)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (T1S1_METJA | Q57594)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0006304    DNA modification    The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties.
    GO:0009307    DNA restriction-modification system    A defense process found in many bacteria and archaea that protects the organism from invading foreign DNA by cleaving it with a restriction endonuclease. The organism's own DNA is protected by methylation of a specific nucleotide, which occurs immediately following replication, in the same target site as the restriction enzyme.

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