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(-) Description

Title :  CRYSTAL STRUCTURE OF TTHA0657-SAM COMPLEX
 
Authors :  K. Murayama, T. Terada, S. Kuramitsu, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  07 May 07  (Deposition) - 13 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Trefoil Knot, Transferase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Murayama, T. Terada, S. Kuramitsu, M. Shirouzu, S. Yokoyama
Crystal Structure Of Ttha0657-Sam Complex
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN TTHA0657
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Synonym: METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2SAM2Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
2SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
2SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2SAM2Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:158 , HIS A:159 , VAL A:160 , VAL A:180 , GLY A:181 , PRO A:182 , GLU A:183 , GLY A:184 , GLY A:185 , VAL A:202 , LEU A:204 , GLY A:205 , ARG A:207 , ILE A:208 , LEU A:209 , ALA A:214BINDING SITE FOR RESIDUE SAM A 300
2AC2SOFTWAREALA B:158 , HIS B:159 , VAL B:160 , VAL B:180 , GLY B:181 , PRO B:182 , GLU B:183 , GLY B:184 , GLY B:185 , LEU B:204 , GLY B:205 , ARG B:207 , LEU B:209 , ALA B:214BINDING SITE FOR RESIDUE SAM B 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z0Y)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:52 -Pro A:53
2Pro A:53 -Pro A:54

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z0Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z0Y)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z0Y)

(-) 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:224
 aligned with Q5SKI6_THET8 | Q5SKI6 from UniProtKB/TrEMBL  Length:228

    Alignment length:224
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224    
         Q5SKI6_THET8     5 RAFSPGLTGVLPLRETRHLVEVLRARVGDRFTVFDGEREALAEVVDLGPPLRYRVLEERRPEREVGVEVVLYVALLKGDKLAEVVRAATELGATRIQPLVTRHSVPKEMGEGKLRRLRAVALEAAKQSGRVVVPEVLPPIPLKAVPQVAQGLVAHVGATARVREVLDPEKPLALAVGPEGGFAEEEVALLEARGFTPVSLGRRILRAETAALALLALCTAGEGR 228
               SCOP domains d2z0ya1 A:5-66 Hypothetical protein TTHA0657 (TT1575)         d2z0ya2 A:67-228 Hypothetical protein TTHA0657 (TT1575)                                                                                                            SCOP domains
               CATH domains 2z0yA01 A:5-66 Hypothetical PUA domain-like; domain 1         2z0yA02 A:67-228  [code=3.40.1280.10, no name defined]                                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee........hhhhhhhhhh..........eee....eee...............eee.........eeeeee....hhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhhhh.........ee...ee.hhh.....eeee......hhhhh......eeeee......hhhhhhhhhh..eeee.......hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z0y A   5 RAFSPGLTGVLPLRETRHLVEVLRARVGDRFTVFDGEREALAEVVDLGPPLRYRVLEERRPEREVGVEVVLYVALLKGDKLAEVVRAATELGATRIQPLVTRHSVPKEmGEGKLRRLRAVALEAAKQSGRVVVPEVLPPIPLKAVPQVAQGLVAHVGATARVREVLDPEKPLALAVGPEGGFAEEEVALLEARGFTPVSLGRRILRAETAALALLALCTAGEGR 228
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224    
                                                                                                                                      113-MSE                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:174
 aligned with Q5SKI6_THET8 | Q5SKI6 from UniProtKB/TrEMBL  Length:228

    Alignment length:174
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224    
         Q5SKI6_THET8    55 LRYRVLEERRPEREVGVEVVLYVALLKGDKLAEVVRAATELGATRIQPLVTRHSVPKEMGEGKLRRLRAVALEAAKQSGRVVVPEVLPPIPLKAVPQVAQGLVAHVGATARVREVLDPEKPLALAVGPEGGFAEEEVALLEARGFTPVSLGRRILRAETAALALLALCTAGEGR 228
               SCOP domains ------------d2z0yb1 B:67-228 Hypothetical protein TTHA0657 (TT1575)                                                                                                            SCOP domains
               CATH domains ------------2z0yB01 B:67-228  [code=3.40.1280.10, no name defined]                                                                                                             CATH domains
           Pfam domains (1) Methyltrans_RNA-2z0yB01 B:55-224                                                                                                                                          ---- Pfam domains (1)
           Pfam domains (2) Methyltrans_RNA-2z0yB02 B:55-224                                                                                                                                          ---- Pfam domains (2)
         Sec.struct. author ..................eeeee.....hhhhhhhhhhhhh...ee..ee.........hhhhhhhhhhhhhhhhhhhh.....ee...ee.........eeee......hhhhh......eeeee......hhhhhhhhhhhheeee.......hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2z0y B  55 LRYRVLEERRPEREVGVEVVLYVALLKGDKLAEVVRAATELGATRIQPLVTRHSVPKEmGEGKLRRLRAVALEAAKQSGRVVVPEVLPPIPLKAVPQVAQGLVAHVGATARVREVLDPEKPLALAVGPEGGFAEEEVALLEARGFTPVSLGRRILRAETAALALLALCTAGEGR 228
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224    
                                                                                    113-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, 3)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: SPOUT (28)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5SKI6_THET8 | Q5SKI6)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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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