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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE METHYLTRANSFERASE (TEHB, STM1608) FROM SALMONELLA TYPHIMURIUM LT2 AT 1.90 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  28 Aug 06  (Deposition) - 12 Sep 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  S-Adenosyl-L-Methionine-Dependent Methyltransferase Fold, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Methyltransferase (16420133) From Salmonella Typhimurium Lt2 At 1. 90 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE METHYLTRANSFERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 16420133
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 48)

Asymmetric Unit (5, 48)
No.NameCountTypeFull Name
1ACY4Ligand/IonACETIC ACID
2CL2Ligand/IonCHLORIDE ION
3EDO8Ligand/Ion1,2-ETHANEDIOL
4MLY18Mod. Amino AcidN-DIMETHYL-LYSINE
5MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (4, 24)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2CL-1Ligand/IonCHLORIDE ION
3EDO6Ligand/Ion1,2-ETHANEDIOL
4MLY9Mod. Amino AcidN-DIMETHYL-LYSINE
5MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (4, 22)
No.NameCountTypeFull Name
1ACY3Ligand/IonACETIC ACID
2CL-1Ligand/IonCHLORIDE ION
3EDO2Ligand/Ion1,2-ETHANEDIOL
4MLY9Mod. Amino AcidN-DIMETHYL-LYSINE
5MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:103 , MSE A:106 , ALA A:134 , ALA A:135BINDING SITE FOR RESIDUE CL A 199
02AC2SOFTWAREVAL B:103 , VAL B:104 , MSE B:105 , MSE B:106 , ALA B:134 , ALA B:135BINDING SITE FOR RESIDUE CL B 199
03AC3SOFTWARELEU A:15 , ASN A:41 , SER A:64 , ASN A:67 , LEU A:68 , ILE A:71 , HOH A:237 , HOH A:271BINDING SITE FOR RESIDUE EDO A 200
04AC4SOFTWAREALA A:30 , PRO A:31 , ASP A:97 , GLY A:127 , TYR A:129 , ACY A:206 , HOH A:254BINDING SITE FOR RESIDUE EDO A 201
05AC5SOFTWAREGLU B:170BINDING SITE FOR RESIDUE EDO B 200
06AC6SOFTWARETYR A:13 , GLY A:14 , ASN B:41 , ARG B:43 , HOH B:232 , HOH B:388BINDING SITE FOR RESIDUE EDO B 201
07AC7SOFTWARETHR A:82 , HOH A:310BINDING SITE FOR RESIDUE EDO A 202
08AC8SOFTWAREALA A:26 , MLY A:27 , VAL A:29 , PRO A:31 , HOH A:296BINDING SITE FOR RESIDUE EDO A 203
09AC9SOFTWAREGLY A:32 , ARG A:33 , ASP A:54 , HOH A:384BINDING SITE FOR RESIDUE EDO A 204
10BC1SOFTWAREALA A:49 , ASP A:78 , ASN A:79 , HOH A:359 , HOH A:368BINDING SITE FOR RESIDUE EDO A 205
11BC2SOFTWAREALA B:26 , MLY B:27 , ALA B:30 , PRO B:31BINDING SITE FOR RESIDUE ACY B 202
12BC3SOFTWAREHIS B:19 , VAL B:103BINDING SITE FOR RESIDUE ACY B 203
13BC4SOFTWAREASP A:97 , PRO A:126 , GLY A:127 , GLY A:128 , EDO A:201 , HOH A:404BINDING SITE FOR RESIDUE ACY A 206
14BC5SOFTWAREARG B:33 , GLU B:109 , MLY B:125 , HOH B:259BINDING SITE FOR RESIDUE ACY B 204

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I6G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2I6G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I6G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2I6G)

(-) Exons   (0, 0)

(no "Exon" information available for 2I6G)

(-) Sequences/Alignments

Asymmetric 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:178
 aligned with Q8ZPC3_SALTY | Q8ZPC3 from UniProtKB/TrEMBL  Length:198

    Alignment length:199
                             1                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189         
         Q8ZPC3_SALTY     - -MTVRDENYFTEKYGLTRTHSDVLAAAKVVAPGRTLDLGCGNGRNSLYLAANGYDVTAWDKNPASMANLERIKAAEGLDNLQTDLVDLNTLTFDGEYDFILSTVVMMFLEAQTIPGLIANMQRCTKPGGYNLIVAAMDTPDFPCTVGFPFAFKEGELRRYYEGWDMLKYNEDVGELHRTDENGNRIKLRFATMLARKTA 198
               SCOP domains -d2i6ga1 A:1-198 Putative methyltransferase TehB                                                                                                                                                        SCOP domains
               CATH domains 2i6gA00 A:0-198 Vaccinia Virus protein VP39                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh....hhhhhhhhh.....eeeee....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh....eeeee...........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeee..---------.......hhhhhhh...eeeeeeeee.------------..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i6g A   0 GmTVRDENYFTEkYGLTRTHSDVLAAAkVVAPGRTLDLGCGNGRNSLYLAANGYDVTAWDkNPASmANLERIkAAEGLDNLQTDLVDLNTLTFDGEYDFILSTVVmmFLEAQTIPGLIANmQRCTkPGGYNLIVAAmD---------FPFAFkEGELRRYYEGWDmLkYNEDVG------------kLRFATmLARkTA 198
                             |       9  |     19       |29        39        49        59|    |  69  |     79        89        99     ||109       119|    | 129      || -       149  |    159     | 169   |     -      |189  |   |  
                             |         12-MLY         27-MLY                           60-MLY|     72-MLY                          105-MSE        120-MSE|        136-MSE    147    |          165-MSE 173          186-MLY |   |  
                             1-MSE                                                          65-MSE                                  106-MSE            125-MLY     137            152-MLY        167-MLY                  192-MSE  
                                                                                                                                                                                                                              196-MLY


Chain B from PDB  Type:PROTEIN  Length:199
 aligned with Q8ZPC3_SALTY | Q8ZPC3 from UniProtKB/TrEMBL  Length:198

    Alignment length:199
                             1                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189         
         Q8ZPC3_SALTY     - -MTVRDENYFTEKYGLTRTHSDVLAAAKVVAPGRTLDLGCGNGRNSLYLAANGYDVTAWDKNPASMANLERIKAAEGLDNLQTDLVDLNTLTFDGEYDFILSTVVMMFLEAQTIPGLIANMQRCTKPGGYNLIVAAMDTPDFPCTVGFPFAFKEGELRRYYEGWDMLKYNEDVGELHRTDENGNRIKLRFATMLARKTA 198
               SCOP domains d2i6gb_ B: Putative methyltransferase TehB                                                                                                                                                              SCOP domains
               CATH domains 2i6gB00 B:0-198 Vaccinia Virus protein VP39                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh....hhhhhhhhhhh...eeeee....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh....eeeee...........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeee..................hhhhhhh...eeeeee..eeeeeee.....eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i6g B   0 GmTVRDENYFTEkYGLTRTHSDVLAAAkVVAPGRTLDLGCGNGRNSLYLAANGYDVTAWDkNPASmANLERIkAAEGLDNLQTDLVDLNTLTFDGEYDFILSTVVmmFLEAQTIPGLIANmQRCTkPGGYNLIVAAmDTPDFPCTVGFPFAFkEGELRRYYEGWDmLkYNEDVGELHRTDENGNRIkLRFATmLARkTA 198
                             |       9  |     19       |29        39        49        59|    |  69  |     79        89        99     ||109       119|    | 129      |139       149  |    159     | 169       179      |189  |   |  
                             |         12-MLY         27-MLY                           60-MLY|     72-MLY                          105-MSE        120-MSE|        136-MSE         152-MLY      165-MSE              186-MLY |   |  
                             1-MSE                                                          65-MSE                                  106-MSE            125-MLY                                   167-MLY                  192-MSE  
                                                                                                                                                                                                                              196-MLY
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I6G)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8ZPC3_SALTY | Q8ZPC3)
molecular function
    GO:0008757    S-adenosylmethionine-dependent methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
    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:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0046690    response to tellurium ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tellurium ion stimulus.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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