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(-) Description

Title :  HHAI DNA METHYLTRANSFERASE (T250G MUTANT) COMPLEX WITH OLIGONUCLEOTIDE CONTAINING 2-AMINOPURINE AS A TARGET BASE (GPGC:GMGC) AND SAH
 
Authors :  D. Daujotyte, S. Grazulis
Date :  27 Nov 05  (Deposition) - 14 Dec 05  (Release) - 29 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Base Flipping, Restriction System, Transferase-Dna Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. K. Neely, D. Daujotyte, S. Grazulis, S. W. Magennis, D. T. F. Dryden, S. Klimasauskas, A. C. Jones
Time-Resolved Fluorescence Of 2-Aminopurine As A Probe Of Base Flipping In M. Hhai-Dna Complexes.
Nucleic Acids Res. V. 33 6953 2005
PubMed-ID: 16340006  |  Reference-DOI: 10.1093/NAR/GKI995

(-) Compounds

Molecule 1 - MODIFICATION METHYLASE HHAI
    Chains: A
    EC Number: 2.1.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHH552
    Expression System Strain: ER1727
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: HAEMOPHILUS HAEMOLYTICUS
    Organism Taxid: 726
    Synonym: DNA METHYLTRANSFERASE HHAI, CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI
 
Molecule 2 - 5'-D(*G*GP*AP*TP*GP*(5CM)*GP*CP*TP*GP*AP*C)-3'
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - 5'-D(*G*TP*CP*AP*GP*(2PR)*GP*CP*AP*TP*CP*C)-3'
    Chains: D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ACD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric/Biological Unit (5, 15)
No.NameCountTypeFull Name
12PR1Mod. Nucleotide2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5'-MONOPHOSPHATE
25CM1Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
3GOL5Ligand/IonGLYCEROL
4SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
5SO47Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:199 , HOH A:2118 , HOH A:2172 , HOH A:2218 , HOH A:2219 , HOH A:2220BINDING SITE FOR RESIDUE SO4 A1329
02AC2SOFTWAREPRO A:286 , ASP A:287 , SER A:288BINDING SITE FOR RESIDUE SO4 A1330
03AC3SOFTWARELYS A:193 , ARG A:245 , LYS A:290 , HOH A:2151 , HOH A:2173BINDING SITE FOR RESIDUE SO4 A1331
04AC4SOFTWARELEU A:196 , LEU A:197 , PRO A:198 , ARG A:281BINDING SITE FOR RESIDUE SO4 A1332
05AC5SOFTWARELYS A:114 , ARG A:172 , HOH A:2222BINDING SITE FOR RESIDUE SO4 A1333
06AC6SOFTWAREGLU A:220 , GLN A:221BINDING SITE FOR RESIDUE SO4 A1334
07AC7SOFTWAREMET A:51 , GLY A:269 , PRO A:293BINDING SITE FOR RESIDUE SO4 A1335
08AC8SOFTWAREPHE 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 , TYR A:285 , ASN A:304 , SER A:305 , VAL A:306 , HOH A:2043 , HOH A:2189 , HOH A:2191 , HOH A:2213 , HOH A:2215 , HOH A:2216 , HOH A:2217BINDING SITE FOR RESIDUE SAH A1328
09AC9SOFTWARELYS A:150 , VAL A:151 , LEU A:152 , ASN A:153 , ASP A:156 , TYR A:157 , PRO A:185 , HOH A:2084 , HOH A:2224BINDING SITE FOR RESIDUE GOL A1336
10BC1SOFTWAREGLU A:3 , ILE A:4 , LYS A:5 , ASP A:6 , TYR A:316 , TYR A:327BINDING SITE FOR RESIDUE GOL A1337
11BC2SOFTWARETYR A:316 , LYS A:325 , PRO A:326 , TYR A:327BINDING SITE FOR RESIDUE GOL A1338
12BC3SOFTWAREGLN A:237 , GLY A:238 , GLY A:250 , LYS A:261 , THR A:262 , GLY A:263 , HOH A:2148 , HOH A:2149 , HOH A:2153 , HOH A:2225BINDING SITE FOR RESIDUE GOL A1339
13BC4SOFTWAREGLU A:203 , HIS A:275 , HOH A:2218 , HOH A:2226 , HOH A:2227 , HOH A:2228 , HOH A:2229BINDING SITE FOR RESIDUE GOL A1340

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C7R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2C7R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C7R)

(-) 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 2C7R)

(-) 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 d2c7ra_ A: automated matches                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2c7rA01 A:1-187,A:304-327 Vaccinia Virus protein VP39                                                                                                                                      2c7rA02 A:188-303 DNA Methylase, subunit A, domain 2                                                                2c7rA01                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee....hhhhhhhhhh..eeeee...hhhhhhhhhhhhh.....hhhhhhhhhh....eeeee............hhhhh....hhhhhhhhhhhhh..eeeeeee.hhhh...hhhhhhhhhhhhhh....eeeeee.hhhh.....eeeeeeee.hhhh..............hhhhh..hhhhhhhh.......ee.............eeee........eeee....................eeee..eeee.hhhhhhhhh..........hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh... 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
                 2c7r A   1 MIEIKDKQLTGLRFIDLFAGLGGFRLALESCGAECVYSNEWDKYAQEVYEMNFGEKPEGDITQVNEKTIPDHDILCAGFPCQAFSISGKQKGFEDSRGTLFFDIARIVREKKPKVVFMENVKNFASHDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIPQKRERIYMICFRNDLNIQNFQFPKPFELNTFVKDLLLPDSEVEHLVIDRKDLVMTNQEIEQTTPKTVRLGIVGKGGQGERIYSTRGIAIGLSAYGGGIFAKTGGYLVNGKTRKLHPRECARVMGYPDSYKVHPSTSQAYKQFGNSVVINVLQYIAYNIGSSLNFKPY 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
                                            
                 2c7r C 402 GGATGcGCTGAC 413
                                 | 411  
                               407-5CM  


Chain D from PDB  Type:DNA  Length:12
                                            
                 2c7r D 422 GTCAGgGCATCC 433
                                 | 431  
                               427-2PR
   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 2C7R)

(-) 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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  2c7r
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  MTH1_HAEPH | P05102
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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 2hmy 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

10mh TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH ADOHCY AND HEMIMETHYLATED DEOXYRIBONUCLEIC ACID CONTAINING 5,6-DIHYDRO-5-AZACYTOSINE AT THE TARGET
1fjx STRUCTURE OF TERNARY COMPLEX OF HHAI METHYLTRANSFERASEMUTANT (T250G) IN COMPLEX WITH DNA AND ADOHCY
1hmy HHAI DEOXYRIBONUCLEIC ACID (CYTOSINE-C5-)- METHYLTRANSFERASE COMPLEX WITH S-ADENOSYL-L- METHIONINE
1m0e ZEBULARINE: A NOVEL DNA METHYLATION INHIBITOR THAT FORMS ACOVALENT COMPLEX WITH DNA METHYLTRANSFERASE
1mht COVALENT TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE, DEOXYRIBONUCLEIC ACID AND S- ADENOSYL-L-HOMOCYSTEINE
1skm HHAI METHYLTRANSFERASE IN COMPLEX WITH DNA CONTAINING ANABASIC SOUTH CARBOCYCLIC SUGAR AT ITS TARGET SITE
1svu STRUCTURE OF THE Q237W MUTANT OF HHAI DNAMETHYLTRANSFERASE: AN INSIGHT INTO PROTEIN- PROTEININTERACTIONS
2c7o HHAI DNA METHYLTRANSFERASE COMPLEX WITH 13MER OLIGONUCLEOTIDE CONTAINING 2-AMINOPURINE ADJACENT TO THE TARGET BASE (PCGC:GMGC) AND SAH
2c7p HHAI DNA METHYLTRANSFERASE COMPLEX WITH OLIGONUCLEOTIDE CONTAINING 2-AMINOPURINE OPPOSITE TO THE TARGET BASE (GCGC:GMPC) AND SAH
2c7q HHAI DNA METHYLTRANSFERASE COMPLEX WITH OLIGONUCLEOTIDE CONTAINING 2-AMINOPURINE OUTSIDE THE RECOGNITION SEQUENCE (PAIRED WITH G) AND SAH
2hmy BINARY COMPLEX OF HHAI METHYLTRANSFERASE WITH ADOMET FORMED IN THE PRESENCE OF A SHORT NONPSECIFIC DEOXYRIBONUCLEIC ACID OLIGONUCLEOTIDE
3mht TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH UNMODIFIED DEOXYRIBONUCLEIC ACID AND ADOHCY
4mht TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH NATIVE DEOXYRIBONUCLEIC ACID AND ADOHCY
5mht TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH HEMIMETHYLATED DEOXYRIBONUCLEIC ACID AND ADOHCY
6mht TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH ADOHCY AND DEOXYRIBONUCLEIC ACID CONTAINING 4'-THIO-2'DEOXYCYTIDINE AT THE TARGET
7mht CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI/ DEOXYRIBONUCLEIC ACID COMPLEX
8mht CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI/ DEOXYRIBONUCLEIC ACID COMPLEX
9mht CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI/ DEOXYRIBONUCLEIC ACID COMPLEX