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(-) Description

Title :  CRYSTAL STRUCTURE OF S-ADENOSYLMETHIONINE-DEPENDENT METHYLTRANSFERASE (NP_349143.1) FROM CLOSTRIDIUM ACETOBUTYLICUM AT 2.00 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  22 Mar 07  (Deposition) - 24 Apr 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Np_349143. 1, S-Adenosylmethionine-Dependent Methyltransferase, Methyltransferase Domain, 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 S-Adenosylmethionine-Dependent Methyltransferase (Np_349143. 1) From Clostridium Acetobutylicum At 2. 00 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - S-ADENOSYLMETHIONINE-DEPENDENT METHYLTRANSFERASE
    Atcc: 824
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NP_349143.1, CA_C2531
    Organism Scientific: CLOSTRIDIUM ACETOBUTYLICUM
    Organism Taxid: 1488
    Strain: DSM 792, JCM 1419, LMG 5710, VKM B-1787

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 21)

Asymmetric/Biological Unit (5, 21)
No.NameCountTypeFull Name
1GOL7Ligand/IonGLYCEROL
2MSE7Mod. Amino AcidSELENOMETHIONINE
3PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
4PGE1Ligand/IonTRIETHYLENE GLYCOL
5SO43Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:180 , ARG A:184 , HOH A:217 , HOH A:243 , HOH A:246 , HOH A:330 , ARG B:12BINDING SITE FOR RESIDUE SO4 A 209
02AC2SOFTWAREARG A:12 , GLN B:7 , PRO B:8 , ARG B:180 , ARG B:184 , HOH B:222 , HOH B:345 , HOH B:391BINDING SITE FOR RESIDUE SO4 B 209
03AC3SOFTWARESER A:161 , LEU A:162 , GLU A:163 , HOH A:225 , HOH A:247 , HOH A:268 , HOH A:269BINDING SITE FOR RESIDUE SO4 A 210
04AC4SOFTWAREGLY A:188 , ILE A:207 , ARG B:151 , LYS B:173BINDING SITE FOR RESIDUE PGE B 210
05AC5SOFTWARELYS A:24 , THR A:25 , GLY A:45 , LYS A:47BINDING SITE FOR RESIDUE PEG A 211
06AC6SOFTWARELYS B:24 , GLY B:45 , LYS B:47BINDING SITE FOR RESIDUE PEG B 211
07AC7SOFTWAREGLU A:183 , ASP B:166 , VAL B:174 , LYS B:177 , HOH B:249 , HOH B:360BINDING SITE FOR RESIDUE PEG B 212
08AC8SOFTWARELEU A:208 , SER B:20 , ASN B:21 , GLY B:120 , LEU B:122 , LEU B:149 , GLU B:201 , HOH B:242 , HOH B:261BINDING SITE FOR RESIDUE GOL B 213
09AC9SOFTWARESER A:65 , LYS A:71 , LEU A:72 , ASN A:73 , ILE A:74BINDING SITE FOR RESIDUE GOL A 212
10BC1SOFTWARESER B:65 , LEU B:72 , ASN B:73 , ILE B:74 , HOH B:375BINDING SITE FOR RESIDUE GOL B 214
11BC2SOFTWAREGLU A:52 , ILE A:53 , HOH A:286 , HOH A:313 , HOH A:316BINDING SITE FOR RESIDUE GOL A 213
12BC3SOFTWARELYS B:131 , SER B:161 , LEU B:162 , GLU B:163 , HOH B:236 , HOH B:315 , HOH B:352 , HOH B:353 , HOH B:396BINDING SITE FOR RESIDUE GOL B 215
13BC4SOFTWAREGLN A:9 , ARG A:12 , GLU A:178 , ARG A:180 , GLN B:9 , ARG B:12 , GLU B:178 , HOH B:222BINDING SITE FOR RESIDUE GOL B 216
14BC5SOFTWAREPHE B:99 , HIS B:100 , GLU B:150 , HIS B:157 , TYR B:195 , HOH B:342BINDING SITE FOR RESIDUE GOL B 217

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P8J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2P8J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P8J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P8J)

(-) Exons   (0, 0)

(no "Exon" information available for 2P8J)

(-) 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:206
 aligned with Q97G40_CLOAB | Q97G40 from UniProtKB/TrEMBL  Length:208

    Alignment length:207
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       
         Q97G40_CLOAB     2 KTIIRQPQLYRFLKYCNESNLDKTVLDCGAGGDLPPLSIFVEDGYKTYGIEISDLQLKKAENFSRENNFKLNISKGDIRKLPFKDESMSFVYSYGTIFHMRKNDVKEAIDEIKRVLKPGGLACINFLTTKDERYNKGEKIGEGEFLQLERGEKVIHSYVSLEEADKYFKDMKVLFKEDRVVERINDGLKIKQGYVDYIAEKFSKSIL 208
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2p8jA00 A:2-208 Vaccinia Virus protein VP39                                                                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh....eeeee.......hhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh....eee............eeeeee..hhhhhhhhhhhhhhhhhhhheeeeeeeeeeeee.........eeee..eeee..-...eeeeeehhhhhhhh....eeeeeeeeeeeeee..eeeeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p8j A   2 KTIIRQPQLYRFLKYCNESNLDKTVLDCGAGGDLPPLSIFVEDGYKTYGIEISDLQLKKAENFSRENNFKLNISKGDIRKLPFKDESmSFVYSYGTIFHmRKNDVKEAIDEIKRVLKPGGLACINFLTTKDERYNKGEKIGEGEFLQLE-GEKVIHSYVSLEEADKYFKDmKVLFKEDRVVERINDGLKIKQGYVDYIAEKFSKSIL 208
                                    11        21        31        41        51        61        71        81       |91       101       111       121       131       141        |-|      161       171|      181       191       201       
                                                                                                                  89-MSE     101-MSE                                          150 |                 172-MSE                                
                                                                                                                                                                                152                                                        


Chain B from PDB  Type:PROTEIN  Length:207
 aligned with Q97G40_CLOAB | Q97G40 from UniProtKB/TrEMBL  Length:208

    Alignment length:207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       
         Q97G40_CLOAB     1 MKTIIRQPQLYRFLKYCNESNLDKTVLDCGAGGDLPPLSIFVEDGYKTYGIEISDLQLKKAENFSRENNFKLNISKGDIRKLPFKDESMSFVYSYGTIFHMRKNDVKEAIDEIKRVLKPGGLACINFLTTKDERYNKGEKIGEGEFLQLERGEKVIHSYVSLEEADKYFKDMKVLFKEDRVVERINDGLKIKQGYVDYIAEKFSKSI 207
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -2p8jB00 B:2-207 Vaccinia Virus protein VP39                                                                                                                                                                    CATH domains
           Pfam domains (1) --------------------------Methyltransf_11-2p8jB01 B:27-125                                                                   ---------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------Methyltransf_11-2p8jB02 B:27-125                                                                   ---------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .......hhhhhhhhhhhhh....eeeee.......hhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh....eee............eeeeee..hhhhhhhhhhhhhhhhhhhheeeeeeeeeeeee.........eeee..eeeeee..eeeeeeeehhhhhhhh....eeeeeeeeeeeeee..eeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p8j B   1 mKTIIRQPQLYRFLKYCNESNLDKTVLDCGAGGDLPPLSIFVEDGYKTYGIEISDLQLKKAENFSRENNFKLNISKGDIRKLPFKDESmSFVYSYGTIFHmRKNDVKEAIDEIKRVLKPGGLACINFLTTKDERYNKGEKIGEGEFLQLERGEKVIHSYVSLEEADKYFKDmKVLFKEDRVVERINDGLKIKQGYVDYIAEKFSKSI 207
                            |       10        20        30        40        50        60        70        80        90       100|      110       120       130       140       150       160       170 |     180       190       200       
                            1-MSE                                                                                  89-MSE     101-MSE                                                                172-MSE
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 2P8J)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q97G40_CLOAB | Q97G40)
molecular function
    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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.

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