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(-) Description

Title :  CRYSTAL STRUCTURE OF A MODIFICATION SUBUNIT OF A PUTATIVE TYPE I RESTRICTION ENZYME FROM VIBRIO VULNIFICUS YJ016
 
Authors :  S. Y. Park, H. J. Lee, J. Sun, K. Nishi, J. M. Song, J. S. Kim
Date :  01 Nov 11  (Deposition) - 07 Nov 12  (Release) - 07 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Methyltransferase Activity, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Y. Park, H. J. Lee, J. M. Song, J. Sun, H. J. Hwang, K. Nishi, J. S. Kim
Structural Characterization Of A Modification Subunit Of A Putative Type I Restriction Enzyme From Vibrio Vulnificus Yj016
Acta Crystallogr. , Sect. D V. 68 1570 2012
PubMed-ID: 23090406  |  Reference-DOI: 10.1107/S0907444912038826

(-) Compounds

Molecule 1 - TYPE I RESTRICTION-MODIFICATION SYSTEM METHYLTRANSFERASE SUBUNIT
    Chains: A
    EC Number: 2.1.1.72
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: VV0266
    Organism Scientific: VIBRIO VULNIFICUS
    Organism Taxid: 196600
    Strain: YJ016

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3UFB)

(-) Sites  (0, 0)

(no "Site" information available for 3UFB)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3UFB)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:82 -Pro A:83
2Ala A:398 -Pro A:399

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UFB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3UFB)

(-) Exons   (0, 0)

(no "Exon" information available for 3UFB)

(-) 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:484
 aligned with Q7MPU6_VIBVY | Q7MPU6 from UniProtKB/TrEMBL  Length:530

    Alignment length:484
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491    
         Q7MPU6_VIBVY    12 ADQPMTTAQQLGAIVKSSRQIMRKDKGLNGDLDRLPMLTWIMFLKFLDDLEQMRETEAVLEGKSFQPAIEAPYRWRDWAAIEGGITGDELIAFINNDEAMRPDGTRGIGLFAYLRSLQGDNGGDRRDVIATVFKGMQNRMINGYLLRDVVDKINGIHFNSSEEMHTLSRLYETMLREMRDAAGDSGEFYTPRPVVRFMVEVMDPQLGESVLDPACGTGGFLVEAFEHLERQCKTVEDREVLQESSIFGGEAKSLPYLLVQMNLLLHGLEYPRIDPENSLRFPLREMGDKDRVDVILTNPPFGGEEEKGILGNFPEDMQTAETAMLFLQLIMRKLKRPGHGSDNGGRAAVVVPNGTLFSDGISARIKEELLKNFNLHTIVRLPEGVFAPYTDIAGNLLFFDRSGPTDDIWYYQITVPEGRKKYTKTKPMESHEFDECLNWWSNRIVNQNAWKESASEIIKYSESGQLIDVNLDRKNPNSLEVLEH 495
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh......hhhhhhhhhhh.eee.....eeehhhhhhhh.......hhhhhhhhhhhh......hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh......eee.....hhhhhhhhhhhhh...hhhhhhhhhh..eeee..hhhhhhhhhhhhhhhh....eee.......hhhhhhhhhh..eeee........hhhhhhhhhhhhh..hhhhhhhhhhhhhh...........eeeeeeehhhhhh.hhhhhhhhhhhhhheeeeeee.............eeeeeee......eeeeee................hhhhhhhhhhhhh.......eeeeehhhheee.....eeee............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ufb A  12 ADQPMTTAQQLGAIVKSSRQIMRKDKGLNGDLDRLPMLTWIMFLKFLDDLEQMRETEAVLEGKSFQPAIEAPYRWRDWAAIEGGITGDELIAFINNDEAMRPDGTRGIGLFAYLRSLQGDNGGDRRDVIATVFKGMQNRMINGYLLRDVVDKINGIHFNSSEEMHTLSRLYETMLREMRDAAGDSGEFYTPRPVVRFMVEVMDPQLGESVLDPACGTGGFLVEAFEHLERQCKTVEDREVLQESSIFGGEAKSLPYLLVQMNLLLHGLEYPRIDPENSLRFPLREMGDKDRVDVILTNPPFGGEEEKGILGNFPEDMQTAETAMLFLQLIMRKLKRPGHGSDNGGRAAVVVPNGTLFSDGISARIKEELLKNFNLHTIVRLPEGVFAPYTDIAGNLLFFDRSGPTDDIWYYQITVPEGRKKYTKTKPMESHEFDECLNWWSNRIVNQNAWKESASEIIKYSESGQLIDVNLDRKNPNSLEVLEH 495
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491
   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 3UFB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UFB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UFB)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q7MPU6_VIBVY | Q7MPU6)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008170    N-methyltransferase activity    Catalysis of the transfer of a methyl group to the nitrogen atom of an acceptor molecule.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006306    DNA methylation    The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.

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  Cis Peptide Bonds
    Ala A:398 - Pro A:399   [ RasMol ]  
    Ala A:82 - Pro A:83   [ RasMol ]  
 

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