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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF TM0872, A PUTATIVE SAM-DEPENDENT METHYLTRANSFERASE, COMPLEXED WITH SAH
 
Authors :  D. J. Miller, W. F. Anderson, Midwest Center For Structural Genomi
Date :  17 Jul 02  (Deposition) - 28 Jan 03  (Release) - 30 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Sam-Dependent Methyltransferase Fold, Protein-Cofactor Product Complex, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. J. Miller, N. Ouellette, E. Evdokimova, A. Savchenko, A. Edwards, W. F. Anderson
Crystal Complexes Of A Predicted S-Adenosylmethionine-Dependent Methyltransferase Reveal A Typical Adomet Binding Domain And A Substrate Recognition Domain
Protein Sci. V. 12 1432 2003
PubMed-ID: 12824489  |  Reference-DOI: 10.1110/PS.0302403

(-) Compounds

Molecule 1 - S-ADENOSYL-METHYLTRANSFERASE MRAW
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: TM0872
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 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  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:199 , LYS A:200 , ARG A:201 , HOH A:556 , HOH A:600BINDING SITE FOR RESIDUE SO4 A 500
2AC2SOFTWAREARG B:199 , LYS B:200 , ARG B:201 , HOH B:507BINDING SITE FOR RESIDUE SO4 B 501
3AC3SOFTWAREHIS A:8 , CYS A:31 , THR A:32 , VAL A:33 , GLY A:34 , GLU A:35 , GLY A:36 , GLY A:37 , HIS A:38 , ASP A:55 , VAL A:56 , SER A:81 , TYR A:82 , ASP A:103 , GLY A:105 , GLN A:110 , MSE A:130 , ASN A:221 , HOH A:508 , HOH A:524 , HOH A:563BINDING SITE FOR RESIDUE SAH A 401
4AC4SOFTWAREHIS B:8 , CYS B:31 , THR B:32 , VAL B:33 , GLY B:34 , GLU B:35 , GLY B:36 , GLY B:37 , HIS B:38 , ASP B:55 , VAL B:56 , VAL B:60 , VAL B:80 , SER B:81 , TYR B:82 , ASP B:103 , GLY B:105 , SER B:107 , GLN B:110 , MSE B:130BINDING SITE FOR RESIDUE SAH B 402

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:46 -A:49
2B:46 -B:49

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg A:175 -Pro A:176
2Arg B:175 -Pro B:176

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M6Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1M6Y)

(-) Exons   (0, 0)

(no "Exon" information available for 1M6Y)

(-) 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:293
 aligned with RSMH_THEMA | Q9WZX6 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:293
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   
           RSMH_THEMA     2 RKYSQRHIPVMVREVIEFLKPEDEKIILDCTVGEGGHSRAILEHCPGCRIIGIDVDSEVLRIAEEKLKEFSDRVSLFKVSYREADFLLKTLGIEKVDGILMDLGVSTYQLKGENRGFTFEREEPLDMRMDLESEVTAQKVLNELPEEELARIIFEYGEEKRFARRIARKIVENRPLNTTLDLVKAVREALPSYEIRRRKRHFATKTFQAIRIYVNRELENLKEFLKKAEDLLNPGGRIVVISFHSLEDRIVKETFRNSKKLRILTEKPVRPSEEEIRENPRARSGRLRAAERI 294
               SCOP domains d1m6ya2 A:2-114,A:216-294 TM0872, methyltransferase domain                                                       d1m6ya1 A:115-215 Putative methyltransferase TM0872, insert domain                                   d1m6ya2 A:2-114,A:216-294 TM0872, methyltransferase domain                      SCOP domains
               CATH domains ------1m6yA01 A:8-113,A:219-294 Vaccinia Virus protein VP39                                                     1m6yA02 A:114-218  [code=1.10.150.170, no name defined]                                                  1m6yA01 A:8-113,A:219-294 Vaccinia Virus protein VP39                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhh.....eeee.....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh....eeeeeee...hhhhhhh.......................hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee.hhhhhhhhhhhhhhh..eee........hhhhhhhhhhhh..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m6y A   2 RKYSQRHIPVmVREVIEFLKPEDEKIILDCTVGEGGHSRAILEHCPGCRIIGIDVDSEVLRIAEEKLKEFSDRVSLFKVSYREADFLLKTLGIEKVDGILmDLGVSTYQLKGENRGFTFEREEPLDmRmDLESEVTAQKVLNELPEEELARIIFEYGEEKRFARRIARKIVENRPLNTTLDLVKAVREALPSYEIRRRKRHFATKTFQAIRIYVNRELENLKEFLKKAEDLLNPGGRIVVISFHSLEDRIVKETFRNSKKLRILTEKPVRPSEEEIRENPRARSGRLRAAERI 294
                                    11|       21        31        41        51        61        71        81        91       101|      111       121      |131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   
                                     12-MSE                                                                                   102-MSE                   128-MSE                                                                                                                                                                  
                                                                                                                                                          130-MSE                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:278
 aligned with RSMH_THEMA | Q9WZX6 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:285
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287     
           RSMH_THEMA     8 HIPVMVREVIEFLKPEDEKIILDCTVGEGGHSRAILEHCPGCRIIGIDVDSEVLRIAEEKLKEFSDRVSLFKVSYREADFLLKTLGIEKVDGILMDLGVSTYQLKGENRGFTFEREEPLDMRMDLESEVTAQKVLNELPEEELARIIFEYGEEKRFARRIARKIVENRPLNTTLDLVKAVREALPSYEIRRRKRHFATKTFQAIRIYVNRELENLKEFLKKAEDLLNPGGRIVVISFHSLEDRIVKETFRNSKKLRILTEKPVRPSEEEIRENPRARSGRLRAAE 292
               SCOP domains d1m6yb2 B:8-114,B:216-292 TM0872, methyltransferase domain                                                 d1m6yb1 B:115-215 Putative methyltransferase TM0872, insert domain                                   d1m6yb2 B:8-114,B:216-292 TM0872, methyltransferase domain                    SCOP domains
               CATH domains 1m6yB01 B:8-113,B:219-292 Vaccinia Virus protein VP39                                                     1m6yB02 B:114-218  [code=1.10.150.170, no name defined]                                                  1m6yB01 B:8-113,B:219-292 Vaccinia Virus protein VP39                      CATH domains
           Pfam domains (1) Methyltransf_5-1m6yB01 B:8-292                                                                                                                                                                                                                                                                Pfam domains (1)
           Pfam domains (2) Methyltransf_5-1m6yB02 B:8-292                                                                                                                                                                                                                                                                Pfam domains (2)
         Sec.struct. author ........hhhhhh.....eeee.......hhhhhhhhh...eeeee..hhhhhhhhhh....hhh.eeee.....hhhhhhhhh....eeeeeee...hhhhhhhh......................hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee.hhhhhhhhhhhhhh....ee.........-------......eeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m6y B   8 HIPVmVREVIEFLKPEDEKIILDCTVGEGGHSRAILEHCPGCRIIGIDVDSEVLRIAEEKLKEFSDRVSLFKVSYREADFLLKTLGIEKVDGILmDLGVSTYQLKGENRGFTFEREEPLDmRmDLESEVTAQKVLNELPEEELARIIFEYGEEKRFARRIARKIVENRPLNTTLDLVKAVREALPSYEIRRRKRHFATKTFQAIRIYVNRELENLKEFLKKAEDLLNPGGRIVVISFHSLEDRIVKETFRNSKKLRILTEKPVRPS-------PRARSGRLRAAE 292
                                |   17        27        37        47        57        67        77        87        97    |  107       117       127| |    137       147       157       167       177       187       197       207       217       227       237       247       257       267     |   -   |   287     
                               12-MSE                                                                                   102-MSE                   128-MSE                                                                                                                                          273     281           
                                                                                                                                                    130-MSE
   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  (2, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RSMH_THEMA | Q9WZX6)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0071424    rRNA (cytosine-N4-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N4-methylcytosine.
    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:0070475    rRNA base methylation    The addition of a methyl group to an atom in the nucleoside base portion of a nucleotide residue in an rRNA molecule.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        RSMH_THEMA | Q9WZX6: 1n2x

(-) Related Entries Specified in the PDB File

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