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(-) Description

Title :  CRYSTAL STRUCTURE OF T. MARITIMA COBALAMIN-INDEPENDENT METHIONINE SYNTHASE COMPLEXED WITH ZN2+ AND HOMOCYSTEINE (MONOCLINIC)
 
Authors :  R. Pejchal, J. L. Smith, M. L. Ludwig
Date :  19 Dec 07  (Deposition) - 11 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Mete, Transferase, Tim Barrel, Homocysteine, Zinc, Zinc Inversion, Amino-Acid Biosynthesis, Metal-Binding, Methionine Biosynthesis, Methyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Koutmos, R. Pejchal, T. M. Bomer, R. G. Matthews, J. L. Smith, M. L. Ludwig
Metal Active Site Elasticity Linked To Activation Of Homocysteine In Methionine Synthases.
Proc. Natl. Acad. Sci. Usa V. 105 3286 2008
PubMed-ID: 18296644  |  Reference-DOI: 10.1073/PNAS.0709960105
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5-METHYLTETRAHYDROPTEROYLTRIGLUTAMATE- HOMOCYSTEINE METHYLTRANSFERASE
    Chains: A, B
    EC Number: 2.1.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-151/D-TOPO
    Expression System Strain: BL21 STAR (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: METE
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: METHIONINE SYNTHASE, VITAMIN-B12 INDEPENDENT ISOZYME, COBALAMIN-INDEPENDENT METHIONINE SYNTHASE

 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, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2HCS2Ligand/Ion2-AMINO-4-MERCAPTO-BUTYRIC ACID
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2HCS1Ligand/Ion2-AMINO-4-MERCAPTO-BUTYRIC ACID
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2HCS1Ligand/Ion2-AMINO-4-MERCAPTO-BUTYRIC ACID
3ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:618 , CYS A:620 , CYS A:704BINDING SITE FOR RESIDUE ZN A 800
2AC2SOFTWAREHIS B:618 , CYS B:620 , CYS B:704BINDING SITE FOR RESIDUE ZN B 801
3AC3SOFTWAREILE A:409 , GLY A:410 , SER A:411 , GLU A:462 , MET A:529 , ASP A:577 , HIS A:618 , CYS A:704 , GLY A:705 , HOH A:967BINDING SITE FOR RESIDUE HCS A 802
4AC4SOFTWARELYS A:104 , PHE A:106 , LEU A:156 , HOH A:866 , HOH A:1026BINDING SITE FOR RESIDUE EDO A 804
5AC5SOFTWAREILE B:409 , GLY B:410 , SER B:411 , GLU B:462 , MET B:529 , ASP B:577 , HIS B:618 , CYS B:620 , CYS B:704 , GLY B:705 , HOH B:896 , HOH B:967BINDING SITE FOR RESIDUE HCS B 803
6AC6SOFTWARELYS B:104 , PHE B:106 , LEU B:156 , HOH B:835 , HOH B:927BINDING SITE FOR RESIDUE EDO B 805

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BQ5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3BQ5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BQ5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BQ5)

(-) Exons   (0, 0)

(no "Exon" information available for 3BQ5)

(-) 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:709
 aligned with METE_THEMA | Q9X112 from UniProtKB/Swiss-Prot  Length:734

    Alignment length:729
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720         
           METE_THEMA     1 MKAYAFGFPKIGEKREFKKALEDFWKGKITEEQFEEEMNKLRMYMVENYRKNVDVIPSNELSYYDFVLDTAVMVGAVPERFGEYRGLSTYFDMARGGKALEMTKFFNTNYHYLVPEIETEEFYLLENKPLEDYLFFKSKGIETAPWVIGPFTFLYLSKRNGEWIRRPNQMEKLLESLVSVYKEVFEKLVENGCKEILVNEPAFVCDLEKAHWDLILNVYRELSEFPLTVFTYYDSVSDYEACVSLPVKRLHFDFVSNEENLKNLEKHGFPEDKKLVAGVINGRQPWKVDLRKVASLVEKLGASAISNSCPLFHLPVTLELENNLPGGLKEKLAFAKEKLEELKMLKDFLEGKTFDLPNVSFEDFAVDLQAVERVRNLPEDSFRREKEYTERDRIQRERLNLPLFPTTTIGSFPQTPEVRKMRSKYRKGEISKEEYEAFIKEQIKKAIELQEEIGLDVLVHGEFERTDMVEFFAEKLNGIATTQNGWVLSYGSRCYRPPIIYGTVTRPEPMTLKEITYAQSLTEKPVKGMLTGPVTIMSWSYYREDIPEREIAYQIALAINEEVKDLEEAGIKIVQIDEPAFREKAPIKKSKWPEYFEWAINAFNLAANARPETQIHAHMCYSDFNEIIEYIHQLEFDVISIEASRSKGEIISAFENFKGWIKQIGVGVWDIHSPAVPSINEMREIVERVLRVLPKELIWINPDCGLKTRNWDEVIPSLRNMVALAKEMR 729
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3bq5A01 A:1-359,A:483-497  [code=3.20.20.210, no name defined]                                                                                                                                                                                                                                                                                                                3bq5A02 A:367-482,A:498-729  [code=3.20.20.210, no name de             fined]                                       3bq5A01        3bq5A02 A:367-482,A:498-729  [code=3.20.20.210, no name defined]                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...ee......hhhhhhhhhh...hhhhh...hhhhhhhhhhh.....eee......eee.............hhhhhhhhhhhh.....eeeeehhhhhhhh.ee..ee..hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee.hhhhh..hhhhhhhhhhhhhhh....eeee.......hhhhhh.....eeeee....hhhhhhhhhhh.....eeeeeee........hhhhhhhhhhhhh..eeee..hhhhh.............hhhhh.hhhhhhhhhhhhhhhhh.........-------hhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhh..............hhhhhhhhhh-------------hhhhhhhhhhhhhhhhh..............hhhhhh..eeee......eeee..eee...eeeeeee.....hhhhhhhhhh......eeeeehhhhhhhh.ee....hhhhhhhhhhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhh.....eeee......hhhhhhhhh......eeeee..........hhhhhhhhhhhhh...hhh.eeee........hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bq5 A   1 TKAYAFGFPKIGEKREFKKALEDFWKGKITEEQFEEEMNKLRMYMVENYRKNVDVIPSNELSYYDFVLDTAVMVGAVPERFGEYRGLSTYFDMARGGKALEMTKFFNTNYHYLVPEIETEEFYLLENKPLEDYLFFKSKGIETAPWVIGPFTFLYLSKRNGEWIRRPNQMEKLLESLVSVYKEVFEKLVENGCKEILVNEPAFVCDLEKAHWDLILNVYRELSEFPLTVFTYYDSVSDYEACVSLPVKRLHFDFVSNEENLKNLEKHGFPEDKKLVAGVINGRQPWKVDLRKVASLVEKLGASAISNSCPLFHLPVTLELENNLPGGLKEKLAFAKEKLEELKMLKDFLEGKTFDLPNV-------DLQAVERVRNLPEDSFRREKEYTERDRIQRERLNLPLFPTTTIGSFPQTPEVRKMRSK-------------FIKEQIKKAIELQEEIGLDVLVHGEFERTDMVEFFAEKLNGIATTQNGWVLSYGSRCYRPPIIYGTVTRPEPMTLKEITYAQSLTEKPVKGMLTGPVTIMSWSYYREDIPEREIAYQIALAINEEVKDLEEAGIKIVQIDEPAFREKAPIKKSKWPEYFEWAINAFNLAANARPETQIHAHMCYSDFNEIIEYIHQLEFDVISIEASRSKGEIISAFENFKGWIKQIGVGVWDIHSPAVPSINEMREIVERVLRVLPKELIWINPDCGLKTRNWDEVIPSLRNMVALAKEMR 729
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350        |-      |370       380       390       400       410       420   |     -       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720         
                                                                                                                                                                                                                                                                                                                                                                                                359     367                                                      424           438                                                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:722
 aligned with METE_THEMA | Q9X112 from UniProtKB/Swiss-Prot  Length:734

    Alignment length:730
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730
           METE_THEMA     1 MKAYAFGFPKIGEKREFKKALEDFWKGKITEEQFEEEMNKLRMYMVENYRKNVDVIPSNELSYYDFVLDTAVMVGAVPERFGEYRGLSTYFDMARGGKALEMTKFFNTNYHYLVPEIETEEFYLLENKPLEDYLFFKSKGIETAPWVIGPFTFLYLSKRNGEWIRRPNQMEKLLESLVSVYKEVFEKLVENGCKEILVNEPAFVCDLEKAHWDLILNVYRELSEFPLTVFTYYDSVSDYEACVSLPVKRLHFDFVSNEENLKNLEKHGFPEDKKLVAGVINGRQPWKVDLRKVASLVEKLGASAISNSCPLFHLPVTLELENNLPGGLKEKLAFAKEKLEELKMLKDFLEGKTFDLPNVSFEDFAVDLQAVERVRNLPEDSFRREKEYTERDRIQRERLNLPLFPTTTIGSFPQTPEVRKMRSKYRKGEISKEEYEAFIKEQIKKAIELQEEIGLDVLVHGEFERTDMVEFFAEKLNGIATTQNGWVLSYGSRCYRPPIIYGTVTRPEPMTLKEITYAQSLTEKPVKGMLTGPVTIMSWSYYREDIPEREIAYQIALAINEEVKDLEEAGIKIVQIDEPAFREKAPIKKSKWPEYFEWAINAFNLAANARPETQIHAHMCYSDFNEIIEYIHQLEFDVISIEASRSKGEIISAFENFKGWIKQIGVGVWDIHSPAVPSINEMREIVERVLRVLPKELIWINPDCGLKTRNWDEVIPSLRNMVALAKEMRE 730
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3bq5B01 B:1-365,B:483-497  [code=3.20.20.210, no name defined]                                                                                                                                                                                                                                                                                                               3bq5B02 B:366-482,B:498-730  [code=3.20.20.210, no name define  d]                                                   3bq5B01        3bq5B02 B:366-482,B:498-730  [code=3.20.20.210, no name defined]                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.....ee......hhhhhhhhhh...hhhhh...hhhhhhhhhhh.....eee......eee.............hhhhhhhhhhhh.....eeeeehhhhhhhh.ee..ee..hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee.hhhhh..hhhhhhhhhhhhhhh....eeee.......hhhhhh.....eeeee....hhhhhhhhhhh.....eeeeeee........hhhhhhhhhhhhh..eeee..hhhhh.............hhhhh.hhhhhhhhhhhhhhhhh........------..hhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhh..............hhhhhhhhhhhh.--.hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhh..eeee......eeee..eee...eeeeeee.....hhhhhhhhhh......eeeeehhhhhhhh.ee....hhhhhhhhhhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhh.....eeee......hhhhhhhhh......eeeee..........hhhhhhhhhhhhh...hhh.eeee........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bq5 B   1 TKAYAFGFPKIGEKREFKKALEDFWKGKITEEQFEEEMNKLRMYMVENYRKNVDVIPSNELSYYDFVLDTAVMVGAVPERFGEYRGLSTYFDMARGGKALEMTKFFNTNYHYLVPEIETEEFYLLENKPLEDYLFFKSKGIETAPWVIGPFTFLYLSKRNGEWIRRPNQMEKLLESLVSVYKEVFEKLVENGCKEILVNEPAFVCDLEKAHWDLILNVYRELSEFPLTVFTYYDSVSDYEACVSLPVKRLHFDFVSNEENLKNLEKHGFPEDKKLVAGVINGRQPWKVDLRKVASLVEKLGASAISNSCPLFHLPVTLELENNLPGGLKEKLAFAKEKLEELKMLKDFLEGKTFDLPN------AVDLQAVERVRNLPEDSFRREKEYTERDRIQRERLNLPLFPTTTIGSFPQTPEVRKMRSKYRK--ISKEEYEAFIKEQIKKAIELQEEIGLDVLVHGEFERTDMVEFFAEKLNGIATTQNGWVLSYGSRCYRPPIIYGTVTRPEPMTLKEITYAQSLTEKPVKGMLTGPVTIMSWSYYREDIPEREIAYQIALAINEEVKDLEEAGIKIVQIDEPAFREKAPIKKSKWPEYFEWAINAFNLAANARPETQIHAHMCYSDFNEIIEYIHQLEFDVISIEASRSKGEIISAFENFKGWIKQIGVGVWDIHSPAVPSINEMREIVERVLRVLPKELIWINPDCGLKTRNWDEVIPSLRNMVALAKEMRE 730
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       | -    |  370       380       390       400       410       420      |430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730
                                                                                                                                                                                                                                                                                                                                                                                               358    365                                                           427  |                                                                                                                                                                                                                                                                                                            
                                                                                                                                                                                                                                                                                                                                                                                                                                                                       430
   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 3BQ5)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BQ5)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (METE_THEMA | Q9X112)
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: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: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: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.
cellular component
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        METE_THEMA | Q9X112: 1t7l 1xdj 1xpg 1xr2 3bq6

(-) Related Entries Specified in the PDB File

1xdj SAME PROTEIN COMPLEX AT ACIDIC PH, ORTHORHOMBIC CRYSTAL FORM
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3bol
3bq6