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(-) Description

Title :  E. COLI I690C/G743C METH C-TERMINAL FRAGMENT (649-1227)
 
Authors :  M. Koutmos, K. A. Pattridge, M. L. Ludwig
Date :  03 Jan 08  (Deposition) - 01 Apr 08  (Release) - 24 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Meth, Transferase, Reactivation Conformation, H759, Cobalamin, Intermodular Interactions, Amino-Acid Biosynthesis, Cobalt, Metal- Binding, Methionine Biosynthesis, Methyltransferase, S-Adenosyl-L- Methionine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Datta, M. Koutmos, K. A. Pattridge, M. L. Ludwig, R. G. Matthews
A Disulfide-Stabilized Conformer Of Methionine Synthase Reveals An Unexpected Role For The Histidine Ligand Of The Cobalamin Cofactor.
Proc. Natl. Acad. Sci. Usa V. 105 4115 2008
PubMed-ID: 18332423  |  Reference-DOI: 10.1073/PNAS.0800329105

(-) Compounds

Molecule 1 - METHIONINE SYNTHASE
    ChainsA
    EC Number2.1.1.13
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPVB8
    Expression System StrainHMS174(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL ACTIVATION COMPLEX (RESIDUES 649-1227)
    GeneMETH
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    Synonym5-METHYLTETRAHYDROFOLATE-HOMOCYSTEINE METHYLTRANSFERASE, METHIONINE SYNTHASE, VITAMIN-B12- DEPENDENT, MS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1B121Ligand/IonCOBALAMIN

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:759 , GLY A:802 , LEU A:803 , SER A:804 , LEU A:806 , ILE A:807 , THR A:808 , ARG A:823 , GLN A:824 , LEU A:831 , GLY A:833 , GLY A:834 , ALA A:835 , THR A:836 , GLN A:858 , ASN A:859 , ALA A:860 , THR A:863 , MET A:952 , ASP A:1093 , ALA A:1136 , PRO A:1137 , GLY A:1138 , TYR A:1139 , HIS A:1145 , ALA A:1170 , MET A:1171 , PRO A:1173 , GLY A:1174 , SER A:1176 , SER A:1178 , HOH A:1331 , HOH A:1342BINDING SITE FOR RESIDUE B12 A 1301

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:690 -A:743

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:960 -Pro A:961
2Trp A:1172 -Pro A:1173

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1B12_BINDINGPS51332 B12-binding domain profile.METH_ECOLI746-881  1A:746-881
2ADOMET_ACTIVATIONPS50974 AdoMet activation domain profile.METH_ECOLI897-1227  1A:897-1227

(-) Exons   (0, 0)

(no "Exon" information available for 3BUL)

(-) 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:577
 aligned with METH_ECOLI | P13009 from UniProtKB/Swiss-Prot  Length:1227

    Alignment length:577
                                   660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220       
          METH_ECOLI    651 QAEWRSWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEASIETLRNYIDWTPFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRTHVINVSHHLRQQTEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYDAD 1227
               SCOP domains d3bula1 A:651-740 Methionine synthase domain                                              d3bula2 A:741-896 Methionine synthase, C-terminal domain                                                                                                    ----d3bula3 A:901-1227 Methionine synthase SAM-binding domain                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 3bulA01 A:651-737 Methyltransferase                                                    -----3bulA02 A:743-895  [code=3.40.50.280, no name defined]                                                                                                   -----3bulA03 A:901-935,A:996-1227       3bulA04 A:936-995                                           3bulA03 A:901-935,A:996-1227 Cobalamin-dependent Methionine Synthase, domain 1                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee......hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhh...eee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..........hhhhhhhh....hhhhh........eeeeee.hhhhhhh...hhhhhhhh......hhhhhh..hhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeeee..eeeee.......eeeeee..............hhhhhh.hhhhh..eeeeeeeee...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhh................hhhhhhhhhhhhhhhhhhh.ee.....ee...eeeeee..............hhhhhhhhhhhh..hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------B12_BINDING  PDB: A:746-881 UniProt: 746-881                                                                                            ---------------ADOMET_ACTIVATION  PDB: A:897-1227 UniProt: 897-1227                                                                                                                                                                                                                                                                                        PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3bul A  651 QAEWRSWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPCEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEASKEQCKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEASIETLRNYIDWTPFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRTHVINVSHHLRQQTEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYDAD 1227
                                   660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220       

   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  (3, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (4, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (METH_ECOLI | P13009)
molecular function
    GO:0008898    S-adenosylmethionine-homocysteine S-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + L-homocysteine = S-adenosyl-L-homocysteine + L-methionine.
    GO:0031419    cobalamin binding    Interacting selectively and non-covalently with cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008705    methionine synthase activity    Catalysis of the reaction: (6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine = (6S)-5,6,7,8-tetrahydrofolate + L-methionine.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0008276    protein methyltransferase activity    Catalysis of the transfer of a methyl group (CH3-) to a protein.
    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:0044237    cellular metabolic process    The chemical reactions and pathways by which individual cells transform chemical substances.
    GO:0050667    homocysteine metabolic process    The chemical reactions and pathways involving homocysteine, the amino acid alpha-amino-gamma-mercaptobutanoic acid. Homocysteine is an important intermediate in the metabolic reactions of its S-methyl derivative, methionine.
    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.
    GO:0006479    protein methylation    The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
    GO:0042558    pteridine-containing compound metabolic process    The chemical reactions and pathways involving any compound containing pteridine (pyrazino(2,3-dipyrimidine)), e.g. pteroic acid, xanthopterin and folic acid.
    GO:0035999    tetrahydrofolate interconversion    The chemical reactions and pathways by which one-carbon (C1) units are transferred between tetrahydrofolate molecules, to synthesise other tetrahydrofolate molecules.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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 Related Entries

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

UniProtKB/Swiss-Prot
        METH_ECOLI | P130091bmt 1k7y 1k98 1msk 3iv9 3iva

(-) Related Entries Specified in the PDB File

1k7y THE SAME FRAGMENT IN SIMILAR CONFORMATION WITH H759 PRESENT