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(-) Description

Title :  COBALAMIN-DEPENDENT METHIONINE SYNTHASE (1-566) FROM THERMOTOGA MARITIMA COMPLEXED WITH ZN2+
 
Authors :  M. Koutmos, J. L. Smith, M. L. Ludwig
Date :  17 Dec 07  (Deposition) - 11 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Meth, Transferase, Tim Barrel, Zinc, Zinc Inversion, 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-METHYLTETRAHYDROFOLATE S-HOMOCYSTEINE METHYLTRANSFERASE
    Chains: A, B
    EC Number: 2.1.1.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET29A
    Expression System Strain: BL21 DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1HCS1Ligand/Ion2-AMINO-4-MERCAPTO-BUTYRIC ACID
2K2Ligand/IonPOTASSIUM ION
3YT31Ligand/IonYTTRIUM (III) ION
4ZN3Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:207 , ASN A:234 , CYS A:272 , CYS A:273BINDING SITE FOR RESIDUE ZN A 701
2AC2SOFTWARECYS B:207 , CYS B:272 , CYS B:273BINDING SITE FOR RESIDUE ZN B 702
3AC3SOFTWARECYS B:207 , ASN B:234 , CYS B:272 , CYS B:273BINDING SITE FOR RESIDUE ZN B 703
4AC4SOFTWAREASP A:19 , GLY A:20 , GLU A:232 , GLY A:271 , HOH A:745BINDING SITE FOR RESIDUE K A 703
5AC5SOFTWAREASP B:19 , GLY B:20 , LEU B:62 , GLU B:232 , GLY B:271 , HOH B:790BINDING SITE FOR RESIDUE K B 704
6AC6SOFTWAREASP A:253 , GLU A:421 , HOH A:723 , HOH A:804 , HOH A:1059BINDING SITE FOR RESIDUE YT3 A 705
7AC7SOFTWAREALA B:21 , TYR B:22 , GLY B:23 , ASP B:105 , GLU B:146 , THR B:147 , HOH B:729 , HOH B:951BINDING SITE FOR RESIDUE HCS B 710

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:114 -Pro A:115
2Tyr B:114 -Pro B:115

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BOL)

(-) 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:557
 aligned with Q9WYA5_THEMA | Q9WYA5 from UniProtKB/TrEMBL  Length:768

    Alignment length:558
                                    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        
         Q9WYA5_THEMA     1 MRNRREVSKLLSERVLLLDGAYGTEFMKYGYDDLPEELNIKAPDVVLKVHRSYIESGSDVILTNTFGATRMKLRKHGLEDKLDPIVRNAVRIARRAAGEKLVFGDIGPTGELPYPLGSTLFEEFYENFRETVEIMVEEGVDGIIFETFSDILELKAAVLAAREVSRDVFLIAHMTFDEKGRSLTGTDPANFAITFDELDIDALGINCSLGPEEILPIFQELSQYTDKFLVVEPNAGKPIVENGKTVYPLKPHDFAVHIDSYYELGVNIFGGCCGTTPEHVKLFRKVLGNRKPLQRKKKRIFAVSSPSKLVTFDHFVVIGERINPAGRKKLWAEMQKGNEEIVIKEAKTQVEKGAEVLDVNFGIESQIDVRYVEKIVQTLPYVSNVPLSLDIQNVDLTERALRAYPGRSLFNSAKVDEEELEMKINLLKKYGGTLIVLLMGKDVPKSFEERKEYFEKALKILERHDFSDRVIFDPGVLPLGAEGKPVEVLKTIEFISSKGFNTTVGLSNLSFGLPDRSYYNTAFLVLGISKGLSSAIMNPLDETLMKTLNATLVILEKK 558
               SCOP domains d3bola2 A:1-300 Cobalamin-dependent methionine synthase MetH, N-terminal domain                                                                                                                                                                                                                             d3bola1 A:301-558 Cobalamin-dependent methionine synthase MetH, C-terminal domain                                                                                                                                                                                  SCOP domains
               CATH domains 3bolA01 A:1-300  [code=3.20.20.330, no name defined]                                                                                                                                                                                                                                                        3bolA02 A:301-558 Dihydropteroate (DHP) synthetase                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.ee....hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.............hhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh....eeeee............hhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhh..eeeee......eee..eee...hhhhhhhhhhhhhhh...ee......hhhhhhhhhhhhh.............eee....eee....eeeeeee....hhhhhhhhhhh.hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhhhhhhhhhhh.hhh.eeee....hhhhh.hhhhhhhhhhhhhhh......hhhhhh.-..hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3bol A   1 MRNRREVSKLLSERVLLLDGAYGTEFMKYGYDDLPEELNIKAPDVVLKVHRSYIESGSDVILTNTFGATRMKLRKHGLEDKLDPIVRNAVRIARRAAGEKLVFGDIGPTGELPYPLGSTLFEEFYENFRETVEIMVEEGVDGIIFETFSDILELKAAVLAAREVSRDVFLIAHMTFDEKGRSLTGTDPANFAITFDELDIDALGINCSLGPEEILPIFQELSQYTDKFLVVEPNAGKPIVENGKTVYPLKPHDFAVHIDSYYELGVNIFGGCCGTTPEHVKLFRKVLGNRKPLQRKKKRIFAVSSPSKLVTFDHFVVIGERINPAGRKKLWAEMQKGNEEIVIKEAKTQVEKGAEVLDVNFGIESQIDVRYVEKIVQTLPYVSNVPLSLDIQNVDLTERALRAYPGRSLFNSAKVDEEELEMKINLLKKYGGTLIVLLMGKDVPKSFEERKEYFEKALKILERHDFSDRVIFDPGVLPLGAEGKPVEVLKTIEFISSKGFNTTVGLSNLSF-LPDRSYYNTAFLVLGISKGLSSAIMNPLDETLMKTLNATLVILEKK 558
                                    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        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        511 |                                             
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          513                                             


Chain B from PDB  Type:PROTEIN  Length:549
 aligned with Q9WYA5_THEMA | Q9WYA5 from UniProtKB/TrEMBL  Length:768

    Alignment length:560
                                    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
         Q9WYA5_THEMA     1 MRNRREVSKLLSERVLLLDGAYGTEFMKYGYDDLPEELNIKAPDVVLKVHRSYIESGSDVILTNTFGATRMKLRKHGLEDKLDPIVRNAVRIARRAAGEKLVFGDIGPTGELPYPLGSTLFEEFYENFRETVEIMVEEGVDGIIFETFSDILELKAAVLAAREVSRDVFLIAHMTFDEKGRSLTGTDPANFAITFDELDIDALGINCSLGPEEILPIFQELSQYTDKFLVVEPNAGKPIVENGKTVYPLKPHDFAVHIDSYYELGVNIFGGCCGTTPEHVKLFRKVLGNRKPLQRKKKRIFAVSSPSKLVTFDHFVVIGERINPAGRKKLWAEMQKGNEEIVIKEAKTQVEKGAEVLDVNFGIESQIDVRYVEKIVQTLPYVSNVPLSLDIQNVDLTERALRAYPGRSLFNSAKVDEEELEMKINLLKKYGGTLIVLLMGKDVPKSFEERKEYFEKALKILERHDFSDRVIFDPGVLPLGAEGKPVEVLKTIEFISSKGFNTTVGLSNLSFGLPDRSYYNTAFLVLGISKGLSSAIMNPLDETLMKTLNATLVILEKKEL 560
               SCOP domains d3bolb2 B:1-300 Cobalamin-dependent methionine synthase MetH, N-terminal domain                                                                                                                                                                                                                             d3bolb1 B:301-560 Cobalamin-dependent methionine synthase MetH, C-terminal domain                                                                                                                                                                                    SCOP domains
               CATH domains 3bolB01 B:1-300  [code=3.20.20.330, no name defined]                                                                                                                                                                                                                                                        3bolB02 B:301-560 Dihydropteroate (DHP) synthetase                                                                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.ee....hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.............hhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh....eeeee............hhhhhhhhhhh....eeeee...hhhhhhhhhhhhhh....eeeee....----------...hhhhhhhhhhhhhh....ee......hhhhhhhhhhhhh.............eee....eee....eeeeeee....hhhhhhhhhh..hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhhhhhhhhhhh.....eeee....hhhhh.hhhhhhhhhhhhhhh......hhhhh..-..hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bol B   1 MRNRREVSKLLSERVLLLDGAYGTEFMKYGYDDLPEELNIKAPDVVLKVHRSYIESGSDVILTNTFGATRMKLRKHGLEDKLDPIVRNAVRIARRAAGEKLVFGDIGPTGELPYPLGSTLFEEFYENFRETVEIMVEEGVDGIIFETFSDILELKAAVLAAREVSRDVFLIAHMTFDEKGRSLTGTDPANFAITFDELDIDALGINCSLGPEEILPIFQELSQYTDKFLVVEPNAG----------YPLKPHDFAVHIDSYYELGVNIFGGCCGTTPEHVKLFRKVLGNRKPLQRKKKRIFAVSSPSKLVTFDHFVVIGERINPAGRKKLWAEMQKGNEEIVIKEAKTQVEKGAEVLDVNFGIESQIDVRYVEKIVQTLPYVSNVPLSLDIQNVDLTERALRAYPGRSLFNSAKVDEEELEMKINLLKKYGGTLIVLLMGKDVPKSFEERKEYFEKALKILERHDFSDRVIFDPGVLPLGAEGKPVEVLKTIEFISSKGFNTTVGLSNLSF-LPDRSYYNTAFLVLGISKGLSSAIMNPLDETLMKTLNATLVILEKKEL 560
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230     |   -      |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
                                                                                                                                                                                                                                                                     236        247                                                                                                                                                                                                                                                                     511 |                                               
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          513
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 4)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9WYA5_THEMA | Q9WYA5)
molecular function
    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: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:0044237    cellular metabolic process    The chemical reactions and pathways by which individual cells transform chemical substances.
    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: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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q9WYA5_THEMA | Q9WYA5: 1q7m 1q7q 1q7z 1q85 1q8a 1q8j 3bof

(-) Related Entries Specified in the PDB File

1q7z SAME PROTEIN COMPLEXED WITH CD2+ INSTEAD OF ZN2+
3bof
3bq5
3bq6