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(-) Description

Title :  STRUCTURE OF THE PTERIN-BINDING DOMAIN METR OF 5-METHYLTETRAHYDROFOLATE-HOMOCYSTEINE METHYLTRANSFERASE FROM BACTEROIDES THETAIOTAOMICRON
 
Authors :  M. E. Cuff, H. Li, G. Cobb, A. Joachimiak, Midwest Center For Structu Genomics (Mcsg)
Date :  25 Sep 09  (Deposition) - 22 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  5-Methyltetrahydrofolate, Methyltransferase, Tim Barrel, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Cuff, H. Li, G. Cobb, A. Joachimiak
Structure Of The Pterin-Binding Domain Metr Of 5-Methyltetrahydrofolate-Homocysteine Methyltransferase Fro Bacteroides Thetaiotaomicron
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 5-METHYLTETRAHYDROFOLATE-HOMOCYSTEINE METHYLTRANSFERASE
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: MODIFIED BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: SEQUENCE DATABASE RESIDUES 345-641
    Gene: BT_0180
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON
    Organism Taxid: 818
    Strain: VPI-5482

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 44)

Asymmetric Unit (5, 44)
No.NameCountTypeFull Name
1GOL10Ligand/IonGLYCEROL
2K2Ligand/IonPOTASSIUM ION
3MSE24Mod. Amino AcidSELENOMETHIONINE
4NA5Ligand/IonSODIUM ION
5THH3Ligand/IonN-[4-({[(6S)-2-AMINO-4-HYDROXY-5-METHYL-5,6,7,8-TETRAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GLUTAMIC ACID
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2K-1Ligand/IonPOTASSIUM ION
3MSE8Mod. Amino AcidSELENOMETHIONINE
4NA-1Ligand/IonSODIUM ION
5THH1Ligand/IonN-[4-({[(6S)-2-AMINO-4-HYDROXY-5-METHYL-5,6,7,8-TETRAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GLUTAMIC ACID
Biological Unit 2 (3, 13)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2K-1Ligand/IonPOTASSIUM ION
3MSE8Mod. Amino AcidSELENOMETHIONINE
4NA-1Ligand/IonSODIUM ION
5THH1Ligand/IonN-[4-({[(6S)-2-AMINO-4-HYDROXY-5-METHYL-5,6,7,8-TETRAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GLUTAMIC ACID
Biological Unit 3 (3, 12)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2K-1Ligand/IonPOTASSIUM ION
3MSE8Mod. Amino AcidSELENOMETHIONINE
4NA-1Ligand/IonSODIUM ION
5THH1Ligand/IonN-[4-({[(6S)-2-AMINO-4-HYDROXY-5-METHYL-5,6,7,8-TETRAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GLUTAMIC ACID

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE B:450 , ALA B:476 , ASP B:515 , ASN C:512 , HIS C:514 , HOH C:705BINDING SITE FOR RESIDUE GOL C 1
02AC2SOFTWAREASN B:512 , HIS C:514BINDING SITE FOR RESIDUE GOL B 1
03AC3SOFTWAREASN B:361 , ALA B:363 , ASN B:561 , PHE B:564 , ARG B:567 , THH B:643BINDING SITE FOR RESIDUE GOL B 642
04AC4SOFTWAREASN C:361 , ALA C:363 , ASN C:561 , PHE C:564 , THH C:643BINDING SITE FOR RESIDUE GOL C 642
05AC5SOFTWAREASN A:512 , HIS A:514 , HIS A:554 , MSE A:591BINDING SITE FOR RESIDUE GOL A 1
06AC6SOFTWAREHOH A:53 , HOH A:89 , HOH A:124 , GLU A:358 , GLY A:364 , SER A:365 , ARG A:366 , ASP A:431 , ASN A:452 , MSE A:480 , ASP A:519 , GLY A:558 , SER A:560 , ASN A:561 , PHE A:564 , ARG A:567 , ARG A:573 , ILE A:593 , GOL A:643 , K A:645 , HOH A:718 , HOH A:748BINDING SITE FOR RESIDUE THH A 642
07AC7SOFTWAREHOH B:23 , HOH B:27 , GLU B:358 , ASN B:361 , GLY B:364 , ARG B:366 , ASP B:431 , ASN B:452 , MSE B:480 , ASP B:519 , GLY B:558 , SER B:560 , ASN B:561 , PHE B:564 , ARG B:567 , ARG B:573 , ILE B:593 , GOL B:642 , NA B:644 , HOH B:721 , HOH B:749BINDING SITE FOR RESIDUE THH B 643
08AC8SOFTWAREHOH C:30 , HOH C:46 , GLU C:358 , ASN C:361 , GLY C:364 , SER C:365 , ARG C:366 , ASP C:431 , ASN C:452 , MSE C:480 , ASP C:519 , GLY C:558 , SER C:560 , ASN C:561 , PHE C:564 , ARG C:567 , ARG C:573 , ILE C:593 , GOL C:642 , NA C:644 , HOH C:729BINDING SITE FOR RESIDUE THH C 643
09AC9SOFTWAREASN A:361 , ALA A:363 , ASN A:561 , PHE A:564 , THH A:642BINDING SITE FOR RESIDUE GOL A 643
10BC1SOFTWAREGLU A:358 , SER A:560BINDING SITE FOR RESIDUE K A 644
11BC2SOFTWARESER A:365 , THH A:642BINDING SITE FOR RESIDUE K A 645
12BC3SOFTWARESER B:365 , THH B:643BINDING SITE FOR RESIDUE NA B 644
13BC4SOFTWARESER C:365 , THH C:643BINDING SITE FOR RESIDUE NA C 644
14BC5SOFTWAREHOH C:109 , ARG C:621 , ARG C:627BINDING SITE FOR RESIDUE GOL C 645
15BC6SOFTWAREHOH B:247 , ARG B:621 , ARG B:627BINDING SITE FOR RESIDUE GOL B 645
16BC7SOFTWAREHOH A:310 , ARG A:621 , ARG A:627BINDING SITE FOR RESIDUE GOL A 646
17BC8SOFTWAREHOH B:265 , ASN B:355BINDING SITE FOR RESIDUE GOL B 646
18BC9SOFTWAREHOH A:282 , ASP A:401 , LEU A:404 , HOH A:757BINDING SITE FOR RESIDUE NA A 647
19CC1SOFTWAREHOH B:58 , ASP B:401 , LEU B:404 , HOH B:649BINDING SITE FOR RESIDUE NA B 647
20CC2SOFTWAREASP C:401 , LEU C:404 , HOH C:761 , HOH C:762BINDING SITE FOR RESIDUE NA C 646

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K13)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asn A:452 -Ser A:453
2Asn B:452 -Ser B:453
3Asn C:452 -Ser C:453

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K13)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K13)

(-) Exons   (0, 0)

(no "Exon" information available for 3K13)

(-) 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:286
 aligned with Q8ABD0_BACTN | Q8ABD0 from UniProtKB/TrEMBL  Length:915

    Alignment length:287
                                   359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       
         Q8ABD0_BACTN   350 EINFVNIGERCNVAGSRKFLRLVNEKKYDEALSIARQQVEDGALVIDVNMDDGLLDARTEMTTFLNLIMSEPEIARVPVMIDSSKWEVIEAGLKCLQGKSIVNSISLKEGEEVFLEHARIIKQYGAATVVMAFDEKGQADTAARKIEVCERAYRLLVDKVGFNPHDIIFDPNVLAVATGIEEHNNYAVDFIEATGWIRKNLPGAHVSGGVSNLSFSFRGNNYIREAMHAVFLYHAIQQGMDMGIVNPGTSVLYSDIPADTLEKIEDVVLNRRPDAAERLIELAEALK 636
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee...hhhhhhhhhh.hhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhh.eeeee.ee..ee..hhhhhhhhhhhhhhhhhhhh..hhh.eeee.........hhhhhhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeee...-..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k13 A 350 EINFVNIGERCNVAGSRKFLRLVNEKKYDEALSIARQQVEDGALVIDVNmDDGLLDARTEmTTFLNLImSEPEIARVPVmIDSSKWEVIEAGLKCLQGKSIVNSISLKEGEEVFLEHARIIKQYGAATVVmAFDEKGQADTAARKIEVCERAYRLLVDKVGFNPHDIIFDPNVLAVATGIEEHNNYAVDFIEATGWIRKNLPGAHVSGGVSNLSFSFRGNNYIREAmHAVFLYHAIQQGmDmGIVNPG-SVLYSDIPADTLEKIEDVVLNRRPDAAERLIELAEALK 636
                                   359       369       379       389       399       409|      419       429       439       449       459       469       479|      489       499       509       519       529       539       549       559       569      |579       589 |     599       609       619       629       
                                                                           399-MSE    410-MSE 418-MSE    429-MSE                                            480-MSE                                                                                         576-MSE      589-MSE 597 |                                     
                                                                                                                                                                                                                                                                           591-MSE 599                                     


Chain B from PDB  Type:PROTEIN  Length:286
 aligned with Q8ABD0_BACTN | Q8ABD0 from UniProtKB/TrEMBL  Length:915

    Alignment length:287
                                   359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       
         Q8ABD0_BACTN   350 EINFVNIGERCNVAGSRKFLRLVNEKKYDEALSIARQQVEDGALVIDVNMDDGLLDARTEMTTFLNLIMSEPEIARVPVMIDSSKWEVIEAGLKCLQGKSIVNSISLKEGEEVFLEHARIIKQYGAATVVMAFDEKGQADTAARKIEVCERAYRLLVDKVGFNPHDIIFDPNVLAVATGIEEHNNYAVDFIEATGWIRKNLPGAHVSGGVSNLSFSFRGNNYIREAMHAVFLYHAIQQGMDMGIVNPGTSVLYSDIPADTLEKIEDVVLNRRPDAAERLIELAEALK 636
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee...hhhhhhhhhh.hhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh.eeeee.ee..ee..hhhhhhhhhhhhhhhhhhhh..hhh.eeee.........hhhhhhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeee...-..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k13 B 350 EINFVNIGERCNVAGSRKFLRLVNEKKYDEALSIARQQVEDGALVIDVNmDDGLLDARTEmTTFLNLImSEPEIARVPVmIDSSKWEVIEAGLKCLQGKSIVNSISLKEGEEVFLEHARIIKQYGAATVVmAFDEKGQADTAARKIEVCERAYRLLVDKVGFNPHDIIFDPNVLAVATGIEEHNNYAVDFIEATGWIRKNLPGAHVSGGVSNLSFSFRGNNYIREAmHAVFLYHAIQQGmDmGIVNPG-SVLYSDIPADTLEKIEDVVLNRRPDAAERLIELAEALK 636
                                   359       369       379       389       399       409|      419       429       439       449       459       469       479|      489       499       509       519       529       539       549       559       569      |579       589 |     599       609       619       629       
                                                                           399-MSE    410-MSE 418-MSE    429-MSE                                            480-MSE                                                                                         576-MSE      589-MSE 597 |                                     
                                                                                                                                                                                                                                                                           591-MSE 599                                     


Chain C from PDB  Type:PROTEIN  Length:287
 aligned with Q8ABD0_BACTN | Q8ABD0 from UniProtKB/TrEMBL  Length:915

    Alignment length:288
                                   359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629        
         Q8ABD0_BACTN   350 EINFVNIGERCNVAGSRKFLRLVNEKKYDEALSIARQQVEDGALVIDVNMDDGLLDARTEMTTFLNLIMSEPEIARVPVMIDSSKWEVIEAGLKCLQGKSIVNSISLKEGEEVFLEHARIIKQYGAATVVMAFDEKGQADTAARKIEVCERAYRLLVDKVGFNPHDIIFDPNVLAVATGIEEHNNYAVDFIEATGWIRKNLPGAHVSGGVSNLSFSFRGNNYIREAMHAVFLYHAIQQGMDMGIVNPGTSVLYSDIPADTLEKIEDVVLNRRPDAAERLIELAEALKE 637
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---Pterin_bind-3k13C01 C:353-565                                                                                                                                                                                        ------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ---Pterin_bind-3k13C02 C:353-565                                                                                                                                                                                        ------------------------------------------------------------------------ Pfam domains (2)
           Pfam domains (3) ---Pterin_bind-3k13C03 C:353-565                                                                                                                                                                                        ------------------------------------------------------------------------ Pfam domains (3)
         Sec.struct. author ....eeeeeeee...hhhhhhhhhh.hhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh.eeeee.ee..ee..hhhhhhhhhhhhhhhhhhhh..hhh.eeee.........hhhhhhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeee...-..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3k13 C 350 EINFVNIGERCNVAGSRKFLRLVNEKKYDEALSIARQQVEDGALVIDVNmDDGLLDARTEmTTFLNLImSEPEIARVPVmIDSSKWEVIEAGLKCLQGKSIVNSISLKEGEEVFLEHARIIKQYGAATVVmAFDEKGQADTAARKIEVCERAYRLLVDKVGFNPHDIIFDPNVLAVATGIEEHNNYAVDFIEATGWIRKNLPGAHVSGGVSNLSFSFRGNNYIREAmHAVFLYHAIQQGmDmGIVNPG-SVLYSDIPADTLEKIEDVVLNRRPDAAERLIELAEALKE 637
                                   359       369       379       389       399       409|      419       429       439       449       459       469       479|      489       499       509       519       529       539       549       559       569      |579       589 |     599       609       619       629        
                                                                           399-MSE    410-MSE 418-MSE    429-MSE                                            480-MSE                                                                                         576-MSE      589-MSE 597 |                                      
                                                                                                                                                                                                                                                                           591-MSE 599
   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 3K13)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K13)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q8ABD0_BACTN | Q8ABD0)
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: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: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.
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.

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    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
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  Q8ABD0_BACTN | Q8ABD0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3K13)