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(-) Description

Title :  CRYSTAL STRUCTURE OF STREPTOCOCCUS MUTANS METE COMPLEXED WITH ZINC
 
Authors :  T. M. Fu, Y. H. Liang, X. D. Su
Date :  19 Jul 11  (Deposition) - 03 Aug 11  (Release) - 28 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym./Biol. Unit :  A
Keywords :  Mete, Barrel, Methyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. M. Fu, J. Almqvist, Y. H. Liang, L. Li, Y. Huang, X. D. Su
Crystal Structures Of Cobalamin-Independent Methionine Synthase (Mete) From Streptococcus Mutans: A Dynamic Zinc-Inversion Model
J. Mol. Biol. V. 412 688 2011
PubMed-ID: 21840320  |  Reference-DOI: 10.1016/J.JMB.2011.08.005

(-) Compounds

Molecule 1 - 5-METHYLTETRAHYDROPTEROYLTRIGLUTAMATE--HOMOCYSTEINE METHYLTRANSFERASE
    Chains: A
    EC Number: 2.1.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: METE
    Organism Scientific: STREPTOCOCCUS MUTANS
    Organism Taxid: 1309
    Strain: UA159
    Synonym: COBALAMIN-INDEPENDENT METHIONINE SYNTHASE, METHIONINE SYNTHASE, VITAMIN-B12 INDEPENDENT ISOZYME

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
2ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:15 , ARG A:16 , PHE A:495 , HOH A:789 , HOH A:1049 , HOH A:1058BINDING SITE FOR RESIDUE SO4 A 746
2AC2SOFTWARELYS A:19 , ARG A:504 , ALA A:505 , HOH A:858 , HOH A:1195BINDING SITE FOR RESIDUE SO4 A 747
3AC3SOFTWAREPHE A:36 , ASP A:89 , ILE A:90 , HOH A:1029 , HOH A:1185 , HOH A:1238BINDING SITE FOR RESIDUE SO4 A 748
4AC4SOFTWAREHIS A:630 , CYS A:632 , GLU A:654 , CYS A:715BINDING SITE FOR RESIDUE ZN A 749

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3T0C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3T0C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3T0C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3T0C)

(-) Exons   (0, 0)

(no "Exon" information available for 3T0C)

(-) 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:737
 aligned with METE_STRMU | Q8CWX6 from UniProtKB/Swiss-Prot  Length:745

    Alignment length:744
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739    
           METE_STRMU     - -MTKVSSLGYPRLGENREWKKLIEAYWAGKVSKNDLFAGAKELRLDFLKKQLNAGLDLIPVGDFSLYDHILDLSVQFNIIPKRFAKEPIDIDLYFAIARGNKENVASSMKKWFNTNYHYIVPEWSKQRPKLNNNRLLDLYLEAREVVGDKAKPVITGPITYVALSTGVEDFTAAVKSLLPLYKQVFTELVKAGASYIQVDEPIFVTDEGKDYLQAAKAVYAYFAKEVPDAKFIFQTYFEGLIDSQVLSQLPVDAFGLDFVYGLEENLEAIKTGAFKGKEIFAGVIDGRNIWSSDFVKTSALLETIEEQSAALTIQPSCSLLHVPVTTKNETDLDPVLRNGLAFADEKLTEVKRLAEHLDGREDPAYDLHIAHFDALQAADFRNVKLEDLSRVATKRPSDFAKRRDIQQEKLHLPLLPTTTIGSFPQSREIRRTRLAWKRGDISDAEYKQFIQAEIERWIRIQEDLDLDVLVHGEFERVDMVEFFGQKLAGFTTTKFGWVQSYGSRAVKPPIIYGDVQHLEPITVEETVYAQSLTDRPVKGMLTGPITITNWSFERTDIPRDQLFNQIGLAIKDEIKLLENAGIAIIQVDEAALREGLPLRKSKQKAYLDDAVHAFHIATSSVKDETQIHTHMCYSKFDEIIDAIRALDADVISIETSRSHGDIIESFETAVYPLGIGLGVYDIHSPRVPTKEEVVANIERPLRQLSPTQFWVNPDCGLKTRQEPETIAALKVLVAATKEVRQKL 743
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee...........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh....eee......hhhhhhhhhhh..hhhhh....hhhhhhhhhhh.-......eee......eee.............hhhhhhhhhhhhhhh..eeeeeehhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhh.....eeeee...hhhhhhhhhhh......eeeeeee........hhhhhhhhhhhhhhh..eeeeee..hhhhh..........hhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh....hhhhh......hhhhhhhhhhhhhh...............--.....-..--...hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhh.eeeee......eeee..eee...eeeeeeee....hhhhhhhhhh......eeeeehhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhh..hhhhhhhhhhhhhhhhhhhhh......eeeeee.......hhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhhh..hhh.eeee........hhhhhhhhhh-hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3t0c A   0 SMTKVSSLGYPRLGENREWKKLIEAYWAGKVSKNDLFAGAKELRLDFLKKQLNAGLDLIPVGDFSLYDHILDLSVQFNIIPKRFAKEPIDIDLYFAIARGN-ENVASSMKKWFNTNYHYIVPEWSKQRPKLNNNRLLDLYLEAREVVGDKAKPVITGPITYVALSTGVEDFTAAVKSLLPLYKQVFTELVKAGASYIQVDEPIFVTDEGKDYLQAAKAVYAYFAKEVPDAKFIFQTYFEGLIDSQVLSQLPVDAFGLDFVYGLEENLEAIKTGAFKGKEIFAGVIDGRNIWSSDFVKTSALLETIEEQSAALTIQPSCSLLHVPVTTKNETDLDPVLRNGLAFADEKLTEVKRLAEHLDGREDPAYDLHIAHFDALQAADFRNVKLEDLSRVATKRPSDFAKRRDIQQEKLHLPLLPTTTIGSFPQS--IRRTR-AW--GDISDAEYKQFIQAEIERWIRIQEDLDLDVLVHGEFERVDMVEFFGQKLAGFTTTKFGWVQSYGSRAVKPPIIYGDVQHLEPITVEETVYAQSLTDRPVKGMLTGPITITNWSFERTDIPRDQLFNQIGLAIKDEIKLLENAGIAIIQVDEAALREGLPLRKSKQKAYLDDAVHAFHIATSSVKDETQIHTHMCYSKFDEIIDAIRALDADVISIETSRSHGDIIESFETAVYPLGIGLGVYDIHSPRVPTKEEVVANIERPLRQLSPTQFWVNPDCGLKTRQEPETIAALK-LVAATKEVRQKL 743
                                     9        19        29        39        49        59        69        79        89        99| |    109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419      |429   | ||439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729| |    739    
                                                                                                                              100 |                                                                                                                                                                                                                                                                                                                                 426  | 433 ||  |                                                                                                                                                                                                                                                                                                730 |           
                                                                                                                                102                                                                                                                                                                                                                                                                                                                                    429   435|  |                                                                                                                                                                                                                                                                                                  732           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              436  |                                                                                                                                                                                                                                                                                                                
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 439
   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  (0, 0)

(no "SCOP Domain" information available for 3T0C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3T0C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T0C)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (METE_STRMU | Q8CWX6)
molecular function
    GO:0003871    5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity    Catalysis of the reaction: 5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = L-methionine + tetrahydropteroyltri-L-glutamate.
    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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0009086    methionine biosynthetic process    The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.

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 Related Entries

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

UniProtKB/Swiss-Prot
        METE_STRMU | Q8CWX6: 2nq5 3l7r

(-) Related Entries Specified in the PDB File

2nq5 3l7r