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(-) Description

Title :  E. COLI METH C-TERMINAL FRAGMENT (649-1227)
 
Authors :  V. Bandarian, K. A. Pattridge, B. W. Lennon, D. P. Huddler, R. G. Matthew M. L. Ludwig
Date :  22 Oct 01  (Deposition) - 21 Dec 01  (Release) - 24 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Motion Of 4-Helix Bundle, Domain Interactions, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Bandarian, K. A. Pattridge, B. W. Lennon, D. P. Huddler, R. G. Matthews, M. L. Ludwig
Domain Alternation Switches B(12)-Dependent Methionine Synthase To The Activation Conformation.
Nat. Struct. Biol. V. 9 53 2002
PubMed-ID: 11731805  |  Reference-DOI: 10.1038/NSB738

(-) Compounds

Molecule 1 - METHIONINE SYNTHASE
    Chains: A
    EC Number: 2.1.1.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRC99A
    Expression System Strain: XL1-BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL ACTIVATION COMPLEX, RESIDUES 651-1227
    Gene: ESCHERICHIA COLI
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1B121Ligand/IonCOBALAMIN
2SO410Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:712 , HIS A:927 , ARG A:928BINDING SITE FOR RESIDUE SO4 A 254
02AC2SOFTWARESO4 A:282 , LYS A:755 , PRO A:785 , ALA A:786 , GLU A:787 , ASN A:816BINDING SITE FOR RESIDUE SO4 A 255
03AC3SOFTWAREARG A:928 , GLN A:932 , ARG A:1106 , TYR A:1111BINDING SITE FOR RESIDUE SO4 A 267
04AC4SOFTWARETYR A:1139 , B12 A:1248BINDING SITE FOR RESIDUE SO4 A 323
05AC5SOFTWARELYS A:720 , ARG A:723 , TYR A:1083BINDING SITE FOR RESIDUE SO4 A 251
06AC6SOFTWARELYS A:819 , LYS A:1188BINDING SITE FOR RESIDUE SO4 A 259
07AC7SOFTWAREARG A:823 , PRO A:1140 , B12 A:1248BINDING SITE FOR RESIDUE SO4 A 260
08AC8SOFTWAREARG A:996 , HIS A:1160BINDING SITE FOR RESIDUE SO4 A 270
09AC9SOFTWARESO4 A:255 , ARG A:1127BINDING SITE FOR RESIDUE SO4 A 282
10BC1SOFTWAREVAL A:971BINDING SITE FOR RESIDUE SO4 A 309
11BC2SOFTWARESO4 A:260 , HOH A:271 , HOH A:279 , SO4 A:323 , VAL A:758 , GLY A:762 , ILE A:765 , VAL A:766 , GLY A:802 , LEU A:803 , SER A:804 , LEU A:806 , ILE A:807 , THR A:808 , LEU A:831 , GLY A:833 , GLY A:834 , ALA A:835 , THR A:836 , VAL A:857 , GLN A:858 , ASN A:859 , ALA A:860 , THR A:863 , ASP A:1093 , ALA A:1136 , PRO A:1137 , GLY A:1138 , TYR A:1139 , PRO A:1140 , HIS A:1145 , ALA A:1170 , MET A:1171 , GLY A:1174 , ALA A:1175 , SER A:1176 , VAL A:1177 , SER A:1178BINDING SITE FOR RESIDUE B12 A 1248

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K7Y)

(-) 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 1K7Y)

(-) 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 1K7Y)

(-) 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 d1k7ya1 A:651-740 Methionine synthase domain                                              d1k7ya2 A:741-900 Methionine synthase, C-terminal domain                                                                                                        d1k7ya3 A:901-1227 Methionine synthase SAM-binding domain                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1k7yA03 A:651-737 Methyltransferase                                                    -----1k7yA01 A:743-895  [code=3.40.50.280, no name defined]                                                                                                   -----1k7yA02 A:901-935,A:996-1227       1k7yA04 A:936-995                                           1k7yA02 A:901-935,A:996-1227 Cobalamin-dependent Methionine Synthase, domain 1                                                                                                                                                           CATH domains
               Pfam domains ------B12-binding_2-1k7yA02 A:657-734                                               ------------B12-binding-1k7yA01 A:747-851                                                                            -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Met_synt_B12-1k7yA03 A:1055-1192                                                                                                          ----------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee......hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhh.....eeee......hhhhhhhhhhh...eee..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhh.................eeeee..hhhhhhhhhhhhhhhhhh......hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeeee..eeeee.......eeeeee..............hhhhhh.hhhhh..eeeeeeeee...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhh................hhhhhhhhhhhhhhhhhh..ee.....ee...eeeeee..............hhhhhhhhhhhhh.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
                1k7y A  651 QAEWRSWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVGDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEASIETLRNYIDWTPFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRTHVINVSHHLRQQTEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYDAD 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
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (4, 4)

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

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: B12-binding] (9)
(-)
Clan: no clan defined [family: B12-binding_2] (2)
(-)
Clan: no clan defined [family: Met_synt_B12] (4)

(-) 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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  1k7y
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  2.1.1.13
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 Related Entries

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

UniProtKB/Swiss-Prot
        METH_ECOLI | P13009: 1bmt 1k98 1msk 3bul 3iv9 3iva

(-) Related Entries Specified in the PDB File

1bmt ENTRY FOR THE B12-BINDING FRAGMENT (651-896)
1msk ENTRY FOR THE ACTIVATION DOMAIN (900-1227)