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(-) Description

Title :  COBALAMIN-DEPENDENT METHIONINE SYNTHASE (1-566) FROM T. MARITIMA (OXIDIZED, ORTHORHOMBIC)
 
Authors :  J. C. Evans, D. P. Huddler, M. T. Hilgers, G. Romanchuk, R. G. Matthews, M. L. Ludwig
Date :  19 Aug 03  (Deposition) - 23 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Homocysteine, Methionine, Folate, Cobalamin, Vitamin B12, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. C. Evans, D. P. Huddler, M. T. Hilgers, G. Romanchuk, R. G. Matthews, M. L. Ludwig
Structures Of The N-Terminal Modules Imply Large Domain Motions During Catalysis By Methionine Synthase.
Proc. Natl. Acad. Sci. Usa V. 101 3729 2004
PubMed-ID: 14752199  |  Reference-DOI: 10.1073/PNAS.0308082100
(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
    Fragment: METH_TM (RESIDUES 1-566)
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1Q7Q)

(-) Sites  (0, 0)

(no "Site" information available for 1Q7Q)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:207 -A:272

(-) Cis Peptide Bonds  (2, 2)

Asymmetric 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 1Q7Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q7Q)

(-) Exons   (0, 0)

(no "Exon" information available for 1Q7Q)

(-) 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:565
 aligned with Q9WYA5_THEMA | Q9WYA5 from UniProtKB/TrEMBL  Length:768

    Alignment length:565
                                    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 MRNRREVSKLLSERVLLLDGAYGTEFMKYGYDDLPEELNIKAPDVVLKVHRSYIESGSDVILTNTFGATRMKLRKHGLEDKLDPIVRNAVRIARRAAGEKLVFGDIGPTGELPYPLGSTLFEEFYENFRETVEIMVEEGVDGIIFETFSDILELKAAVLAAREVSRDVFLIAHMTFDEKGRSLTGTDPANFAITFDELDIDALGINCSLGPEEILPIFQELSQYTDKFLVVEPNAGKPIVENGKTVYPLKPHDFAVHIDSYYELGVNIFGGCCGTTPEHVKLFRKVLGNRKPLQRKKKRIFAVSSPSKLVTFDHFVVIGERINPAGRKKLWAEMQKGNEEIVIKEAKTQVEKGAEVLDVNFGIESQIDVRYVEKIVQTLPYVSNVPLSLDIQNVDLTERALRAYPGRSLFNSAKVDEEELEMKINLLKKYGGTLIVLLMGKDVPKSFEERKEYFEKALKILERHDFSDRVIFDPGVLPLGAEGKPVEVLKTIEFISSKGFNTTVGLSNLSFGLPDRSYYNTAFLVLGISKGLSSAIMNPLDETLMKTLNATLVILEKKELPRAEV 565
               SCOP domains d1q7qa2 A:1-300 Cobalamin-dependent methionine synthase MetH, N-terminal domain                                                                                                                                                                                                                             d1q7qa1 A:301-565 Cobalamin-dependent methionine synthase MetH, C-terminal domain                                                                                                                                                                                         SCOP domains
               CATH domains 1q7qA01 A:1-300  [code=3.20.20.330, no name defined]                                                                                                                                                                                                                                                        1q7qA02 A:301-565 Dihydropteroate (DHP) synthetase                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.ee....hhhhhhh........hhhhhhhhhhhhhhhhhhhhh..eee......hhhhhhhh....hhhhhhhhhhhhhhhhhh..eeeeee.............hhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh....eeeee............hhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeee.................hhhhhhhhhhhhhhh...ee......hhhhhhhhhhhhh.............eee....eee....eeee.......hhhhhhhhhhh.hhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh....ee.....hhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhhhhhhhhhhh.hhh.eeee...........hhhhhhhhhhhhhhh.ee..hhhhh.....hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q7q A   1 MRNRREVSKLLSERVLLLDGAYGTEFMKYGYDDLPEELNIKAPDVVLKVHRSYIESGSDVILTNTFGATRMKLRKHGLEDKLDPIVRNAVRIARRAAGEKLVFGDIGPTGELPYPLGSTLFEEFYENFRETVEIMVEEGVDGIIFETFSDILELKAAVLAAREVSRDVFLIAHMTFDEKGRSLTGTDPANFAITFDELDIDALGINCSLGPEEILPIFQELSQYTDKFLVVEPNAGKPIVENGKTVYPLKPHDFAVHIDSYYELGVNIFGGCCGTTPEHVKLFRKVLGNRKPLQRKKKRIFAVSSPSKLVTFDHFVVIGERINPAGRKKLWAEMQKGNEEIVIKEAKTQVEKGAEVLDVNFGIESQIDVRYVEKIVQTLPYVSNVPLSLDIQNVDLTERALRAYPGRSLFNSAKVDEEELEMKINLLKKYGGTLIVLLMGKDVPKSFEERKEYFEKALKILERHDFSDRVIFDPGVLPLGAEGKPVEVLKTIEFISSKGFNTTVGLSNLSFGLPDRSYYNTAFLVLGISKGLSSAIMNPLDETLMKTLNATLVILEKKELPRAEV 565
                                    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     


Chain B from PDB  Type:PROTEIN  Length:552
 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 d1q7qb2 B:1-300 Cobalamin-dependent methionine synthase MetH, N-terminal domain                                                                                                                                                                                                                             d1q7qb1 B:301-558 Cobalamin-dependent methionine synthase MetH, C-terminal domain                                                                                                                                                                                  SCOP domains
               CATH domains 1q7qB01 B:1-300  [code=3.20.20.330, no name defined]                                                                                                                                                                                                                                                        1q7qB02 B:301-558 Dihydropteroate (DHP) synthetase                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.ee....hhhhhhh.....hhhhhhh.hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.............hhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhh....eeeee............hhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeee.................hhhhhhhhhhhhhhh...ee......hhhhhhhhhhhhh.............eee....eee....eeee.......hhhhhhhhh...hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhh......ee.....hhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhhhhhhhhhhhhhhh.eeee..........hhhhhhhhhhhhhhh...........------hhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1q7q B   1 MRNRREVSKLLSERVLLLDGAYGTEFMKYGYDDLPEELNIKAPDVVLKVHRSYIESGSDVILTNTFGATRMKLRKHGLEDKLDPIVRNAVRIARRAAGEKLVFGDIGPTGELPYPLGSTLFEEFYENFRETVEIMVEEGVDGIIFETFSDILELKAAVLAAREVSRDVFLIAHMTFDEKGRSLTGTDPANFAITFDELDIDALGINCSLGPEEILPIFQELSQYTDKFLVVEPNAGKPIVENGKTVYPLKPHDFAVHIDSYYELGVNIFGGCCGTTPEHVKLFRKVLGNRKPLQRKKKRIFAVSSPSKLVTFDHFVVIGERINPAGRKKLWAEMQKGNEEIVIKEAKTQVEKGAEVLDVNFGIESQIDVRYVEKIVQTLPYVSNVPLSLDIQNVDLTERALRAYPGRSLFNSAKVDEEELEMKINLLKKYGGTLIVLLMGKDVPKSFEERKEYFEKALKILERHDFSDRVIFDPGVLPLGAEGKPVEVLKTIEFISSKGFNTTVGLSNL------RSYYNTAFLVLGISKGLSSAIMNPLDETLMKTLNATLVILEKK 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        |-     | 520       530       540       550        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      509    516
   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  (2, 4)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Q7Q)

(-) Gene Ontology  (9, 9)

Asymmetric 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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  Cis Peptide Bonds
    Tyr A:114 - Pro A:115   [ RasMol ]  
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  1q7q
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  2.1.1.13
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1q7m COBALAMIN-DEPENDENT METHIONINE SYNTHASE (METH) FROM THERMOTOGA MARITIMA (OXIDIZED, MONOCLINIC)
1q7z COBALAMIN-DEPENDENT METHIONINE SYNTHASE (1-566) FROM THERMOTOGA MARITIMA (CD2+ COMPLEX)
1q85 COBALAMIN-DEPENDENT METHIONINE SYNTHASE (1-566) FROM THERMOTOGA MARITIMA (CD2+ COMPLEX, SE-MET)
1q8a COBALAMIN-DEPENDENT METHIONINE SYNTHASE (1-566) FROM THERMOTOGA MARITIMA (CD2+:L-HCY COMPLEX, SE-MET)