Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  BINARY COMPLEX OF HHAI METHYLTRANSFERASE WITH ADOMET FORMED IN THE PRESENCE OF A SHORT NONPSECIFIC DNA OLIGONUCLEOTIDE
 
Authors :  M. O'Gara, X. Zhang, R. J. Roberts, X. Cheng
Date :  08 Feb 99  (Deposition) - 19 Mar 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.61
Chains :  Asym./Biol. Unit :  B
Keywords :  Transferase (Methyltransferase) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. O'Gara, X. Zhang, R. J. Roberts, X. Cheng
Structure Of A Binary Complex Of Hhai Methyltransferase With S-Adenosyl-L-Methionine Formed In The Presence Of A Short Non-Specific Dna Oligonucleotide.
J. Mol. Biol. V. 287 201 1999
PubMed-ID: 10080885  |  Reference-DOI: 10.1006/JMBI.1999.2608
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI)
    Chains: B
    EC Number: 2.1.1.73
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: HAEMOPHILUS HAEMOLYTICUS
    Organism Taxid: 726

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE B:18 , ALA B:19 , GLY B:20 , LEU B:21 , GLY B:23 , ASN B:39 , GLU B:40 , TRP B:41 , ASP B:60 , ILE B:61 , GLY B:78 , LEU B:100 , TYR B:285 , ASN B:304 , SER B:305 , VAL B:306 , HOH B:376BINDING SITE FOR RESIDUE SAM B 328

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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  1B:12-325
2C5_MTASE_1PS00094 C-5 cytosine-specific DNA methylases active site.MTH1_HAEPH73-85  1B:73-85
3C5_MTASE_2PS00095 C-5 cytosine-specific DNA methylases C-terminal signature.MTH1_HAEPH300-318  1B:300-318

(-) Exons   (0, 0)

(no "Exon" information available for 2HMY)

(-) 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 B 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 d2hmyb_ B: DNA methylase HhaI                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2hmyB01 B:1-186,B:285-327 Vaccinia Virus protein VP39                                                                                                                                     2hmyB02 B:187-284 DNA Methylase, subunit A, domain 2                                              2hmyB01 B:1-186,B:285-327                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee.....hhhhhhhhh..eeeeee...hhhhhhhhhh........hhh..hhh.....eeee...............hhhh....hhhhhhhhhhh...eeeeeeehhh..hhhhhhhhhhhhhhhhh....eeeeeehhh.......eeeeeeee.hhh................hhh....hhhhhhh......................eeee........eee.....................eeee..eeee..hhhhhhhh...........hhhhhhhhhh...hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------SAM_MT_C5  PDB: B:12-325 UniProt: 12-325                                                                                                                                                                                                                                                                                  -- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------C5_MTASE_1   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C5_MTASE_2         --------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hmy B   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
   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 2HMY)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain B   (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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    SAM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2hmy)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2hmy
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MTH1_HAEPH | P05102
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.1.1.73
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  MTH1_HAEPH | P05102
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 2hr1 2i9k 2uyc 2uyh 2uz4 2z6a 2z6q 2z6u 2zcj 3eeo 3mht 4mht 5ciy 5mht 6mht 7mht 8mht 9mht

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2HMY)