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(-) Description

Title :  TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH UNMODIFIED DNA AND ADOHCY
 
Authors :  M. O'Gara, S. Klimasauskas, R. J. Roberts, X. Cheng
Date :  24 Jul 96  (Deposition) - 27 Jan 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Complex (Methyltransferase/Dna), Transferase, Methyltransferase, Restriction System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. O'Gara, S. Klimasauskas, R. J. Roberts, X. Cheng
Enzymatic C5-Cytosine Methylation Of Dna: Mechanistic Implications Of New Crystal Structures For Hhal Methyltransferase-Dna-Adohcy Complexes.
J. Mol. Biol. V. 261 634 1996
PubMed-ID: 8800212  |  Reference-DOI: 10.1006/JMBI.1996.0489
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*GP*AP*TP*AP*GP*CP*GP*CP*TP*AP*TP*C)- 3')
    ChainsC
    EngineeredYES
    SyntheticYES
 
Molecule 2 - DNA (5'- D(*TP*GP*AP*TP*AP*GP*CP*GP*CP*TP*AP*TP*C)-3')
    ChainsD
    EngineeredYES
    SyntheticYES
 
Molecule 3 - PROTEIN (HHAI METHYLTRANSFERASE (E.C.2.1.1.73))
    ChainsA
    Organism ScientificHAEMOPHILUS HAEMOLYTICUS
    Organism Taxid726

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ACD

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
1AC1SOFTWAREPHE A:18 , ALA A:19 , LEU A:21 , GLY A:23 , ASN A:39 , GLU A:40 , TRP A:41 , ASP A:60 , ILE A:61 , GLY A:78 , PRO A:80 , TYR A:285 , ASN A:304 , SER A:305 , HOH A:332 , HOH A:333 , HOH A:374BINDING SITE FOR RESIDUE SAH A 328

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MHT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_C5PS51679 C-5 cytosine-specific DNA methylase (Dnmt) domain profile.MTH1_HAEPH12-325  1A:12-325
2C5_MTASE_1PS00094 C-5 cytosine-specific DNA methylases active site.MTH1_HAEPH73-85  1A:73-85
3C5_MTASE_2PS00095 C-5 cytosine-specific DNA methylases C-terminal signature.MTH1_HAEPH300-318  1A:300-318

(-) Exons   (0, 0)

(no "Exon" information available for 3MHT)

(-) 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:327
 aligned with MTH1_HAEPH | P05102 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:327
                                    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       
           MTH1_HAEPH     1 MIEIKDKQLTGLRFIDLFAGLGGFRLALESCGAECVYSNEWDKYAQEVYEMNFGEKPEGDITQVNEKTIPDHDILCAGFPCQAFSISGKQKGFEDSRGTLFFDIARIVREKKPKVVFMENVKNFASHDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIPQKRERIYMICFRNDLNIQNFQFPKPFELNTFVKDLLLPDSEVEHLVIDRKDLVMTNQEIEQTTPKTVRLGIVGKGGQGERIYSTRGIAITLSAYGGGIFAKTGGYLVNGKTRKLHPRECARVMGYPDSYKVHPSTSQAYKQFGNSVVINVLQYIAYNIGSSLNFKPY 327
               SCOP domains d3mhta_ A: DNA methylase HhaI                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3mhtA01 A:1-186,A:285-327 Vaccinia Virus protein VP39                                                                                                                                     3mhtA02 A:187-284 DNA Methylase, subunit A, domain 2                                              3mhtA01 A:1-186,A:285-327                   CATH domains
               Pfam domains -----------DNA_methylase-3mhtA01 A:12-320                                                                                                                                                                                                                                                                                       ------- Pfam domains
         Sec.struct. author ............eeeee.....hhhhhhhhh..eeeeee...hhhhhhhhhhh.......hhh..hhh.....eeee..............hhh......hhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeehhh.......eeeeeeeee...................hhh....hhhhhhh......eee.............eeeee.......eeee....................eeee..eeee..hhhhhhhh...........hhhhhhhhhh...hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------SAM_MT_C5  PDB: A:12-325 UniProt: 12-325                                                                                                                                                                                                                                                                                  -- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------C5_MTASE_1   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C5_MTASE_2         --------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mht A   1 MIEIKDKQLTGLRFIDLFAGLGGFRLALESCGAECVYSNEWDKYAQEVYEMNFGEKPEGDITQVNEKTIPDHDILCAGFPCQAFSISGKQKGFEDSRGTLFFDIARIVREKKPKVVFMENVKNFASHDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIPQKRERIYMICFRNDLNIQNFQFPKPFELNTFVKDLLLPDSEVEHLVIDRKDLVMTNQEIEQTTPKTVRLGIVGKGGQGERIYSTRGIAITLSAYGGGIFAKTGGYLVNGKTRKLHPRECARVMGYPDSYKVHPSTSQAYKQFGNSVVINVLQYIAYNIGSSLNFKPY 327
                                    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       

Chain C from PDB  Type:DNA  Length:12
                                            
                 3mht C 402 GATAGCGCTATC 413
                                   411  

Chain D from PDB  Type:DNA  Length:13
                                             
                 3mht D 421 TGATAGCGCTATC 433
                                   430   

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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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MTH1_HAEPH | P05102)
molecular function
    GO:0003886    DNA (cytosine-5-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + DNA containing cytosine = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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:0090116    C-5 methylation of cytosine    The covalent transfer of a methyl group to C-5 of cytosine in a DNA molecule.
    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:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MTH1_HAEPH | P0510210mh 1fjx 1hmy 1m0e 1mht 1skm 1svu 2c7o 2c7p 2c7q 2c7r 2hmy 2hr1 2i9k 2uyc 2uyh 2uz4 2z6a 2z6q 2z6u 2zcj 3eeo 4mht 5ciy 5mht 6mht 7mht 8mht 9mht

(-) Related Entries Specified in the PDB File

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