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(-) Description

Title :  PVUII DNA METHYLTRANSFERASE (CYTOSINE-N4-SPECIFIC)
 
Authors :  W. Gong, M. O'Gara, R. M. Blumenthal, X. Cheng
Date :  31 Jul 98  (Deposition) - 12 Aug 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Type Ii Dna-(Cytosine N4) Methyltransferase, Amino Methylation, Selenomethionine, Multiwavelength Anomalous Diffraction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Gong, M. O'Gara, R. M. Blumenthal, X. Cheng
Structure Of Pvu Ii Dna-(Cytosine N4) Methyltransferase, An Example Of Domain Permutation And Protein Fold Assignment.
Nucleic Acids Res. V. 25 2702 1997
PubMed-ID: 9207015  |  Reference-DOI: 10.1093/NAR/25.14.2702
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (N-4 CYTOSINE-SPECIFIC METHYLTRANSFERASE PVU II)
    Chains: A
    EC Number: 2.1.1.113
    Engineered: YES
    Expression System: ESCHERICHIA COLI STR. K-12 SUBSTR. DH10B
    Expression System Strain: DH10B
    Expression System Taxid: 316385
    Fragment: STARTING FROM THE INTERNAL TRANSLATION INITIATOR AT MET14
    Mutation: YES
    Organism Scientific: PROTEUS VULGARIS
    Organism Taxid: 585

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:33 , ASP A:34 , SER A:35 , SER A:53 , PRO A:55 , HIS A:246 , ALA A:248 , ARG A:249 , PHE A:250 , ILE A:272 , PHE A:273 , GLY A:274 , GLY A:275 , SER A:276 , THR A:278 , GLU A:294 , MET A:295 , TYR A:299BINDING SITE FOR RESIDUE SAH A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1N4_MTASEPS00093 N-4 cytosine-specific DNA methylases signature.MTP2_PROHU51-56  1A:51-56

(-) Exons   (0, 0)

(no "Exon" information available for 1BOO)

(-) 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:282
 aligned with MTP2_PROHU | P11409 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:320
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335
           MTP2_PROHU    16 NFGKKPAYTTSNGSMYIGDSLELLESFPDESISLVMTSPPFALQRKKEYGNLEQHEYVDWFLSFAKVVNKKLKPDGSFVVDFGGAYMKGVPARSIYNFRVLIRMIDEVGFFLAEDFYWFNPSKLPSPIEWVNKRKIRVKDAVNTVWWFSKTEWPKSDITKVLAPYSDRMKKLIEDPDKFYTPKTRPSGHDIGKSFSKDNGGSIPPNLLQISNSESNGQYLANCKLMGIKAHPARFPAKLPEFFIRMLTEPDDLVVDIFGGSNTTGLVAERESRKWISFEMKPEYVAASAFRFLDNNISEEKITDIYNRILNGESLDLNSI 335
               SCOP domains d1booa_ A: m.PvuII N4 cytosine-specific DNA methyltransferase                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1booA00 A:16-335 Vaccinia Virus protein VP39                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..eeee..hhhhhhhh......eeeee......................................eeeeeee...ee..eee....................eeeeeee......................eeeeeeee..............--------------------------------------.....eeee...........................hhhhhhhhhh.....eeee......hhhhhhhh...eeeeee..hhhhhhhh.........hhhhhhhhhhhh...eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------N4_MTA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1boo A  16 NFGKKPAYTTSNGSMYIGDSLELLESFPEESISLVMTSPPFALQRKKEYGNLEQHEYVDWFLSFAKVVNKKLKPDGSFVVDFGGAYMKGVPARSIYNFRVLIRMIDEVGFFLAEDFYWFNPSKLPSPIEWVNKRKIRVKDAVNTVWWFSKTEWPKSDITKVLA--------------------------------------SIPPNLLQISNSESNGQYLANCKLMGIKAHPARFPAKLPEFFIRMLTEPDDLVVDIFGGSNTTGLVAERESRKWISFEMKPEYVAASAFRFLDNNISEEKITDIYNRILNGESLDLNSI 335
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175  |      -         -         -         - |     225       235       245       255       265       275       285       295       305       315       325       335
                                                                                                                                                                                            178                                    217
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BOO)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MTP2_PROHU | P11409)
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:0015667    site-specific DNA-methyltransferase (cytosine-N4-specific) activity    Catalysis of the reaction: S-adenosyl-L-methionine + DNA cytosine = S-adenosyl-L-homocysteine + DNA N4-methylcytosine.
    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: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.
    GO:0090124    N-4 methylation of cytosine    The covalent transfer of a methyl group to N-4 of cytosine in a DNA molecule.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.

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