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(-) Description

Title :  5-METHYLTETRAHYDROFOLATE CORRINOID/IRON SULFUR PROTEIN METHYLTRANSFERASE COMPLEXED WITH METHYLTETRAHYDROFOLATE TO 2.2 ANGSROM RESOLUTION
 
Authors :  T. I. Doukov, C. L. Drennan, H. Hemmi, S. W. Ragsdale
Date :  09 Jan 07  (Deposition) - 30 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Methyltetrahydrofolate-Protein Complex, Corrionoid, Vitamin B12, Tim Barrel, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. I. Doukov, H. Hemmi, C. L. Drennan, S. W. Ragsdale
Structural And Kinetic Evidence For An Extended Hydrogen-Bonding Network In Catalysis Of Methyl Group Transfer. Role Of An Active Site Asparagine Residue In Activation Of Methyl Transfer By Methyltransferases.
J. Biol. Chem. V. 282 6609 2007
PubMed-ID: 17172470  |  Reference-DOI: 10.1074/JBC.M609828200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5-METHYLTETRAHYDROFOLATE CORRINOID/IRON SULFUR PROTEIN METHYLTRANSFERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: B834(DE3)PLYSS(MET-)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: METR, ACSE
    Organism Scientific: MOORELLA THERMOACETICA
    Organism Taxid: 1525

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1C2F2Ligand/Ion5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID
2CA2Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:222 , ASP A:224 , HOH A:3032 , HOH A:3053 , HOH A:3059 , HOH A:3095 , HOH A:3210BINDING SITE FOR RESIDUE CA A 3001
2AC2SOFTWARELYS B:184 , GLY B:222 , ASP B:224 , HOH B:4083 , HOH B:4220 , HOH B:4221BINDING SITE FOR RESIDUE CA B 4001
3AC3SOFTWAREGLU A:6 , MET A:11 , PHE A:12 , ASP A:75 , ASN A:96 , ILE A:120 , ASP A:160 , GLY A:196 , SER A:198 , ASN A:199 , GLN A:202 , ARG A:207 , ILE A:227 , HOH A:3002 , HOH A:3003 , HOH A:3054 , HOH A:3148 , HOH A:3176BINDING SITE FOR RESIDUE C2F A 3000
4AC4SOFTWAREMET B:11 , ASP B:75 , ASN B:96 , ILE B:120 , ASP B:160 , GLY B:196 , SER B:198 , ASN B:199 , GLN B:202 , ARG B:207 , HOH B:4002 , HOH B:4003 , HOH B:4036 , HOH B:4066 , HOH B:4120 , HOH B:4213BINDING SITE FOR RESIDUE C2F B 4000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2E7F)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:96 -Ser A:97
2Asp A:188 -Pro A:189
3Asn B:96 -Ser B:97
4Asp B:188 -Pro B:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2E7F)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PTERIN_BINDINGPS50972 Pterin-binding domain profile.ACSE_MOOTH1-246
 		  2A:1-246
B:1-246

(-) Exons   (0, 0)

(no "Exon" information available for 2E7F)

(-) 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:262
 aligned with ACSE_MOOTH | Q46389 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:262
                                    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  
           ACSE_MOOTH     1 MLIIGERINGMFGDIKRAIQERDPAPVQEWARRQEEGGARALDLNVGPAVQDKVSAMEWLVEVTQEVSNLTLCLDSTNIKAIEAGLKKCKNRAMINSTNAEREKVEKLFPLAVEHGAALIGLTMNKTGIPKDSDTRLAFAMELVAAADEFGLPMEDLYIDPLILPANVAQDHAPEVLKTLQQIKMLADPAPKTVLGLSNVSQNCQNRPLINRTFLAMAMACGLDAAIADACDEALIETAATAEILLNQTVYCDSFVKMFKTR 262
               SCOP domains d2e7fa_ A: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2e7fA00 A:1-262 Dihydropteroate (DHP) synthetase                                                                                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhh.eeeee.........hhhhhhhhhhhhhhhhhhhh.hhh.eeee..........hhhhhhhhhhhhhhh......eeeee.hhhhh...hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh.......hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PTERIN_BINDING  PDB: A:1-246 UniProt: 1-246                                                                                                                                                                                                           ---------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e7f A   1 MLIIGERINGMFGDIKRAIQERDPAPVQEWARRQEEGGARALDLNVGPAVQDKVSAMEWLVEVTQEVSNLTLCLDSTNIKAIEAGLKKCKNRAMINSTNAEREKVEKLFPLAVEHGAALIGLTMNKTGIPKDSDTRLAFAMELVAAADEFGLPMEDLYIDPLILPANVAQDHAPEVLKTLQQIKMLADPAPKTVLGLSNVSQNCQNRPLINRTFLAMAMACGLDAAIADACDEALIETAATAEILLNQTVYCDSFVKMFKTR 262
                                    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  


Chain B from PDB  Type:PROTEIN  Length:262
 aligned with ACSE_MOOTH | Q46389 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:262
                                    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  
           ACSE_MOOTH     1 MLIIGERINGMFGDIKRAIQERDPAPVQEWARRQEEGGARALDLNVGPAVQDKVSAMEWLVEVTQEVSNLTLCLDSTNIKAIEAGLKKCKNRAMINSTNAEREKVEKLFPLAVEHGAALIGLTMNKTGIPKDSDTRLAFAMELVAAADEFGLPMEDLYIDPLILPANVAQDHAPEVLKTLQQIKMLADPAPKTVLGLSNVSQNCQNRPLINRTFLAMAMACGLDAAIADACDEALIETAATAEILLNQTVYCDSFVKMFKTR 262
               SCOP domains d2e7fb_ B: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2e7fB00 B:1-262 Dihydropteroate (DHP) synthetase                                                                                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhh.eeeee.........hhhhhhhhhhhhhhhhhhhh.hhh.eeee..........hhhhhhhhhhhhhh.......eeeee.hhhhh...hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh.......hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PTERIN_BINDING  PDB: B:1-246 UniProt: 1-246                                                                                                                                                                                                           ---------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e7f B   1 MLIIGERINGMFGDIKRAIQERDPAPVQEWARRQEEGGARALDLNVGPAVQDKVSAMEWLVEVTQEVSNLTLCLDSTNIKAIEAGLKKCKNRAMINSTNAEREKVEKLFPLAVEHGAALIGLTMNKTGIPKDSDTRLAFAMELVAAADEFGLPMEDLYIDPLILPANVAQDHAPEVLKTLQQIKMLADPAPKTVLGLSNVSQNCQNRPLINRTFLAMAMACGLDAAIADACDEALIETAATAEILLNQTVYCDSFVKMFKTR 262
                                    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
   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  (1, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2E7F)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ACSE_MOOTH | Q46389)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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:0102036    methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase activity    Catalysis of the reaction: a tetrahydrofolate + a [methyl-Co(III) corrinoid Fe-S protein] <=> an N5-methyl-tetrahydrofolate + a [Co(I) corrinoid Fe-S protein]
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0015977    carbon fixation    A metabolic process in which carbon (usually derived from carbon dioxide) is incorporated into organic compounds (usually carbohydrates).
    GO:0044237    cellular metabolic process    The chemical reactions and pathways by which individual cells transform chemical substances.
    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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  2e7f
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  ACSE_MOOTH | Q46389
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 Related Entries

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

UniProtKB/Swiss-Prot
        ACSE_MOOTH | Q46389: 1f6y 2ogy 4djd 4dje 4djf

(-) Related Entries Specified in the PDB File

1ad4 DIHYDROPTEROATE SYNTHASE (DHPS), S. AUREUS, COMPLEXED WITH 7,8-DIHYDRO-6-HYDROXYMETHYL-PTERIN-PYROPHOSPHASE (DHPTPP)
1aj0 DIHYDROPTEROATE SYNTHASE (DHPS), E.COLI, COMPLEXED WITH 7, 8-DIHYDROPTERIN-PYROPHOSPHASE (DHPPP)
1f6y APO STRUCTURE OF THE WILD TYPE CORRINOID-DEPENDENT METHYLTETRAHYDROFOLATE METHYLTRANSFERASE
1q8j METHIONINE SYNTHASE COMPLEX WITH METHYLTETRAHYDROFOLATE
1tww DIHYDROPTEROATE SYNTHASE (DHPS), B. ANTHRACIS, COMPLEXED WITH 6-HYDROXYMETHYL-PTERIN-PYROPHOSPHASE (DHPTPP)
1tx0 DIHYDROPTEROATE SYNTHASE (DHPS), B. ANTHRACIS, COMPLEXED WITH PTEROIC ACID