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(-) Description

Title :  COBALAMIN-DEPENDENT METHIONINE SYNTHASE (1-566) FROM THERMOTOGA MARITIMA (CD2+ COMPLEX, SE-MET)
 
Authors :  J. C. Evans, D. P. Huddler, M. T. Hilgers, G. Romanchuk, R. G. Matthews, M. L. Ludwig
Date :  20 Aug 03  (Deposition) - 23 Mar 04  (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 :  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  (2, 23)

Asymmetric Unit (2, 23)
No.NameCountTypeFull Name
1CD3Ligand/IonCADMIUM ION
2MSE20Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 10)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:207 , ASN A:234 , CYS A:272 , CYS A:273BINDING SITE FOR RESIDUE CD A 601
2AC2SOFTWARECYS B:207 , ASN B:234 , CYS B:272 , CYS B:273BINDING SITE FOR RESIDUE CD B 602
3AC3SOFTWAREASP A:253 , GLU A:421BINDING SITE FOR RESIDUE CD A 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q85)

(-) 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 1Q85)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q85)

(-) Exons   (0, 0)

(no "Exon" information available for 1Q85)

(-) 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:559
 aligned with Q9WYA5_THEMA | Q9WYA5 from UniProtKB/TrEMBL  Length:768

    Alignment length:559
                                    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 MRNRREVSKLLSERVLLLDGAYGTEFMKYGYDDLPEELNIKAPDVVLKVHRSYIESGSDVILTNTFGATRMKLRKHGLEDKLDPIVRNAVRIARRAAGEKLVFGDIGPTGELPYPLGSTLFEEFYENFRETVEIMVEEGVDGIIFETFSDILELKAAVLAAREVSRDVFLIAHMTFDEKGRSLTGTDPANFAITFDELDIDALGINCSLGPEEILPIFQELSQYTDKFLVVEPNAGKPIVENGKTVYPLKPHDFAVHIDSYYELGVNIFGGCCGTTPEHVKLFRKVLGNRKPLQRKKKRIFAVSSPSKLVTFDHFVVIGERINPAGRKKLWAEMQKGNEEIVIKEAKTQVEKGAEVLDVNFGIESQIDVRYVEKIVQTLPYVSNVPLSLDIQNVDLTERALRAYPGRSLFNSAKVDEEELEMKINLLKKYGGTLIVLLMGKDVPKSFEERKEYFEKALKILERHDFSDRVIFDPGVLPLGAEGKPVEVLKTIEFISSKGFNTTVGLSNLSFGLPDRSYYNTAFLVLGISKGLSSAIMNPLDETLMKTLNATLVILEKKE 559
               SCOP domains d1q85a2 A:1-300 Cobalamin-dependent methionine synthase MetH, N-terminal domain                                                                                                                                                                                                                             d1q85a1 A:301-559 Cobalamin-dependent methionine synthase MetH, C-terminal domain                                                                                                                                                                                   SCOP domains
               CATH domains -1q85A01 A:2-300  [code=3.20.20.330, no name defined]                                                                                                                                                                                                                                                       1q85A02 A:301-559 Dihydropteroate (DHP) synthetase                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.ee....hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh....eee......hhhhhh...hhhhhhhhhhhhhhhhhhhhh..eeeeee.............hhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhh....eeeee............hhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhh..eeeee......ee....ee...hhhhhhhhhhhhhhh...ee......hhhhhhhhhhhhh.............eee....eee....eeeeeee....hhhhhhhhhh.hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhh.....ee.....hhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhhhhhhhhhhh.hhh.eeee..........hhhhhhhhhhhhhhh......hhhhh.....hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q85 A   1 mRNRREVSKLLSERVLLLDGAYGTEFmKYGYDDLPEELNIKAPDVVLKVHRSYIESGSDVILTNTFGATRmKLRKHGLEDKLDPIVRNAVRIARRAAGEKLVFGDIGPTGELPYPLGSTLFEEFYENFRETVEImVEEGVDGIIFETFSDILELKAAVLAAREVSRDVFLIAHmTFDEKGRSLTGTDPANFAITFDELDIDALGINCSLGPEEILPIFQELSQYTDKFLVVEPNAGKPIVENGKTVYPLKPHDFAVHIDSYYELGVNIFGGCCGTTPEHVKLFRKVLGNRKPLQRKKKRIFAVSSPSKLVTFDHFVVIGERINPAGRKKLWAEmQKGNEEIVIKEAKTQVEKGAEVLDVNFGIESQIDVRYVEKIVQTLPYVSNVPLSLDIQNVDLTERALRAYPGRSLFNSAKVDEEELEmKINLLKKYGGTLIVLLmGKDVPKSFEERKEYFEKALKILERHDFSDRVIFDPGVLPLGAEGKPVEVLKTIEFISSKGFNTTVGLSNLSFGLPDRSYYNTAFLVLGISKGLSSAImNPLDETLmKTLNATLVILEKKE 559
                            |       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         
                            |                        27-MSE                                      71-MSE                                                         135-MSE                                174-MSE                                                                                                                                                         334-MSE                                                                                 422-MSE          439-MSE                                                                                           537-MSE 545-MSE          
                            1-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:550
 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 d1q85b2 B:1-300 Cobalamin-dependent methionine synthase MetH, N-terminal domain                                                                                                                                                                                                                             d1q85b1 B:301-558 Cobalamin-dependent methionine synthase MetH, C-terminal domain                                                                                                                                                                                  SCOP domains
               CATH domains -1q85B01 B:2-300  [code=3.20.20.330, no name defined]                                                                                                                                                                                                                                                       1q85B02 B:301-558 Dihydropteroate (DHP) synthetase                                                                                                                                                                                                                 CATH domains
           Pfam domains (1) --------------S-methyl_trans-1q85B03 B:15-289                                                                                                                                                                                                                                                    -------------------------Pterin_bind-1q85B01 B:315-512                                                                                                                                                                         ---------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------S-methyl_trans-1q85B04 B:15-289                                                                                                                                                                                                                                                    -------------------------Pterin_bind-1q85B02 B:315-512                                                                                                                                                                         ---------------------------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhh...ee....hhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...eee......hhhhhh...hhhhhhhhhhhhhhhhhhhhh..eeeeee.............hhhhhhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhhhhh....eeeee............hhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeee....--------.....hhhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhh.............eee....eee....eeee.......hhhhhhhhhhh.hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh....ee.....hhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhhhhhhhhhhh.hhh.eeee....hhhhh.hhhhhhhhhhhhhhh......hhhhh.....hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1q85 B   1 mRNRREVSKLLSERVLLLDGAYGTEFmKYGYDDLPEELNIKAPDVVLKVHRSYIESGSDVILTNTFGATRmKLRKHGLEDKLDPIVRNAVRIARRAAGEKLVFGDIGPTGELPYPLGSTLFEEFYENFRETVEImVEEGVDGIIFETFSDILELKAAVLAAREVSRDVFLIAHmTFDEKGRSLTGTDPANFAITFDELDIDALGINCSLGPEEILPIFQELSQYTDKFLVVEPNAG--------TVYPLKPHDFAVHIDSYYELGVNIFGGCCGTTPEHVKLFRKVLGNRKPLQRKKKRIFAVSSPSKLVTFDHFVVIGERINPAGRKKLWAEmQKGNEEIVIKEAKTQVEKGAEVLDVNFGIESQIDVRYVEKIVQTLPYVSNVPLSLDIQNVDLTERALRAYPGRSLFNSAKVDEEELEmKINLLKKYGGTLIVLLmGKDVPKSFEERKEYFEKALKILERHDFSDRVIFDPGVLPLGAEGKPVEVLKTIEFISSKGFNTTVGLSNLSFGLPDRSYYNTAFLVLGISKGLSSAImNPLDETLmKTLNATLVILEKK 558
                            |       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        
                            1-MSE                    27-MSE                                      71-MSE                                                         135-MSE                                174-MSE                                                       236      245                                                                                      334-MSE                                                                                 422-MSE          439-MSE                                                                                           537-MSE 545-MSE
   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  (2, 4)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)
(-)
Clan: no clan defined [family: S-methyl_trans] (7)

(-) 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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  1q85
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1q7m COBALAMIN-DEPENDENT METHIONINE SYNTHASE (METH) FROM THERMOTOGA MARITIMA (OXIDIZED, MONOCLINIC)
1q7q COBALAMIN-DEPENDENT METHIONINE SYNTHASE (1-566) FROM T. MARITIMA (OXIDIZED, ORTHORHOMBIC)
1q7z COBALAMIN-DEPENDENT METHIONINE SYNTHASE (1-566) FROM THERMOTOGA MARITIMA (CD2+ COMPLEX)
1q8a COBALAMIN-DEPENDENT METHIONINE SYNTHASE (1-566) FROM THERMOTOGA MARITIMA (CD2+:L-HCY COMPLEX, SE-MET)