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(-) Description

Title :  TERNARY STRUCTURE OF ARG165ALA M.HHAI C5-CYTOSINE DNA METHYLTRANSFERASE WITH UNMODIFIED DNA AND ADOHCY
 
Authors :  F. K. Shieh
Date :  08 Aug 07  (Deposition) - 28 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.79
Chains :  Asym./Biol. Unit :  A,C,D,E
Keywords :  Beta-Alpha-Complex, Methyltransferase, Restriction System, S-Adenosyl-L-Methionine, Transferase, Transferase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. K. Shieh, B. Youngblood, N. O. Reich
The Role Of Arg165 Towards Base Flipping, Base Stabilization And Catalysis In M. Hhai
J. Mol. Biol. V. 362 516 2006
PubMed-ID: 16926025  |  Reference-DOI: 10.1016/J.JMB.2006.07.030
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MODIFICATION METHYLASE HHAI
    Chains: A
    EC Number: 2.1.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHSHW-5
    Expression System Strain: ER1727
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HHAIM
    Mutation: YES
    Organism Scientific: HAEMOPHILUS PARAHAEMOLYTICUS
    Organism Taxid: 735
    Synonym: HHAI METHYLTRANSFERASE, CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI, M.HHAI
 
Molecule 2 - DNA (5'- D(*DGP*DAP*DTP*DAP*DGP*DCP*DGP*DCP*DTP*DAP*DTP*DC)-3')
    Chains: C
    Engineered: YES
    Other Details: SYNTHETIC CONSTRUCTION
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*DTP*DGP*DAP*DTP*DAP*DG)-3')
    Chains: D
    Engineered: YES
    Other Details: SYNTHETIC CONSTRUCTION
    Synthetic: YES
 
Molecule 4 - DNA (5'-D(*DGP*DCP*DTP*DAP*DTP*DC)-3')
    Chains: E
    Engineered: YES
    Other Details: SYNTHETIC CONSTRUCTION
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ACDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1DCZ1Ligand/Ion2'-DEOXYCYTIDINE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:81 , SER A:85 , GLU A:119 , ASN A:120 , VAL A:121 , ARG A:163 , GLU A:164 , ALA A:165 , THR A:250 , ASN A:304 , HOH A:346 , HOH A:383 , DG D:426 , HOH E:347 , DG E:428BINDING SITE FOR RESIDUE DCZ A 427
2AC2SOFTWAREPHE A:18 , ALA A:19 , LEU A:21 , GLY A:23 , ASN A:39 , GLU A:40 , TRP A:41 , ASP A:42 , ASP A:60 , ILE A:61 , GLY A:78 , PRO A:80 , LEU A:100 , ASN A:304 , SER A:305 , HOH A:338 , HOH A:345 , HOH A:377 , HOH A:385 , DT D:421BINDING SITE FOR RESIDUE SAH A 328

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z6Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Z6Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z6Q)

(-) 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 2Z6Q)

(-) 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 d2z6qa_ A: DNA methylase HhaI                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2z6qA01 A:1-186,A:285-327 Vaccinia Virus protein VP39                                                                                                                                     2z6qA02 A:187-284 DNA Methylase, subunit A, domain 2                                              2z6qA01 A:1-186,A:285-327                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee....hhhhhhhhhh..eeeee...hhhhhhhhhhhhh.....hhhhhhhhhh....eeee.............hhhhh....hhhhhhhhhhhhh..eeeeeehhhhhh...hhhhhhhhhhhhhh....eeeeee.hhh......eeeeeeee.hhhh..............hhhhh..hhhhhh..ee.....ee.............eeee........eee.....................eeee..eee..hhhhhhhhh..........hhhhhhhhhhh..hhhhhhhhhhhhhhhhh.... 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
                 2z6q A   1 MIEIKDKQLTGLRFIDLFAGLGGFRLALESCGAECVYSNEWDKYAQEVYEMNFGEKPEGDITQVNEKTIPDHDILCAGFPCQAFSISGKQKGFEDSRGTLFFDIARIVREKKPKVVFMENVKNFASHDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIPQKREAIYMICFRNDLNIQNFQFPKPFELNTFVKDLLLPDSEVEHLVIDRKDLVMTNQEIEQTTPKTVRLGIVGKGGQGERIYSTRGIAITLSAYGGGIFAKTGGYLVNGKTRKLHPRECARVMGYPDSYKVHPSTSQAYKQFGNSVVINVLQYIAYNIGSSLNFKPY 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
                                            
                 2z6q C 402 GATAGCGCTATC 413
                                   411  


Chain D from PDB  Type:DNA  Length:6
                                      
                 2z6q D 421 TGATAG 426


Chain E from PDB  Type:DNA  Length:6
                                      
                 2z6q E 428 GCTATC 433
   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, 1)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Z6Q)

(-) 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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  2.1.1.37
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 Related Entries

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

UniProtKB/Swiss-Prot
        MTH1_HAEPH | P05102: 10mh 1fjx 1hmy 1m0e 1mht 1skm 1svu 2c7o 2c7p 2c7q 2c7r 2hmy 2hr1 2i9k 2uyc 2uyh 2uz4 2z6a 2z6u 2zcj 3eeo 3mht 4mht 5ciy 5mht 6mht 7mht 8mht 9mht

(-) Related Entries Specified in the PDB File

2hr1 THE STRUCTURE OF WILD TYPE C5-CYTOSINE DNA METHYLTRANSFERASE, M.HHAI