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(-) Description

Title :  METHYLTRANSFERASE BOUND WITH METHYLTETRAHYDROFOLATE
 
Authors :  S. Goetzl, J. -H. Jeoung, S. E. Hennig, H. Dobbek
Date :  16 Mar 11  (Deposition) - 08 Jun 11  (Release) - 03 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Goetzl, J. -H. Jeoung, S. E. Hennig, H. Dobbek
Structural Basis For Electron And Methyl-Group Transfer In A Methyltransferase System Operating In The Reductive Acetyl-Coa Pathway
J. Mol. Biol. V. 411 96 2011
PubMed-ID: 21640123  |  Reference-DOI: 10.1016/J.JMB.2011.05.025

(-) Compounds

Molecule 1 - 5-METHYLTETRAHYDROFOLATE CORRINOID/IRON SULFUR PROTEIN METHYLTRANSFERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28
    Expression System Vector Type: PLASMID
    Organism Scientific: CARBOXYDOTHERMUS HYDROGENOFORMANS
    Organism Taxid: 246194
    Strain: Z-2901
    Synonym: METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1C2F1Ligand/Ion5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID
2GOL3Ligand/IonGLYCEROL
3SO45Ligand/IonSULFATE ION
Biological Unit 1 (3, 18)
No.NameCountTypeFull Name
1C2F2Ligand/Ion5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID
2GOL6Ligand/IonGLYCEROL
3SO410Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:47 , GLY A:48 , THR A:50 , PRO A:54 , MET A:187BINDING SITE FOR RESIDUE SO4 A1264
2AC2SOFTWAREALA A:51 , ASP A:52 , ASP A:53BINDING SITE FOR RESIDUE SO4 A1265
3AC3SOFTWARELYS A:23 , TRP A:60BINDING SITE FOR RESIDUE SO4 A1266
4AC4SOFTWAREARG A:91 , GLY A:92 , HOH A:2068BINDING SITE FOR RESIDUE SO4 A1267
5AC5SOFTWAREPRO A:72 , GLY A:92 , HIS A:93 , HOH A:2156 , HOH A:2157BINDING SITE FOR RESIDUE GOL A1268
6AC6SOFTWAREGLN A:171 , ASN A:248 , ILE A:251BINDING SITE FOR RESIDUE GOL A1269
7AC7SOFTWAREARG A:208 , PRO A:209 , ASN A:212 , ASP A:230 , ASP A:233 , HOH A:2158 , HOH A:2163BINDING SITE FOR RESIDUE GOL A1270
8AC8SOFTWARECYS A:253 , ASP A:254 , SER A:255 , HOH A:2160BINDING SITE FOR RESIDUE SO4 A1271
9AC9SOFTWAREMET A:12 , PHE A:13 , ASP A:76 , ASN A:97 , ASP A:161 , GLY A:197 , ASN A:200 , GLN A:203 , ARG A:208 , ILE A:228 , HOH A:2161 , HOH A:2163BINDING SITE FOR RESIDUE C2F A3000

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:97 -Ser A:98
2Asn A:189 -Pro A:190

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YCJ)

(-) Exons   (0, 0)

(no "Exon" information available for 2YCJ)

(-) 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:271
 aligned with Q3ACR9_CARHZ | Q3ACR9 from UniProtKB/TrEMBL  Length:263

    Alignment length:271
                                    1                                                                                                                                                                                                                                                                      
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262 
         Q3ACR9_CARHZ     - --------MFIMIGERINGMFKDIREAILNKDPRPIQEWARRQAEKGAHYLDVNTGPTADDPVRVMEWLVKTIQEVVDLPCCLDSTNPDAIEAGLKVHRGHAMINSTSADQWKMDIFFPMAKKYEAAIIGLTMNEKGVPKDANDRSQLAMELVANADAHGIPMTELYIDPLILPVNVAQEHAVEVLETIRQIKLMANPAPRTVLGLSNVSQKCPDRPLINRTYLVMAMTAGLDAAIMDVDDDALVDAAATAHILLNKEIYCDSYLKTFRQK 263
               SCOP domains d2ycja_ A: automated matches                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------Pterin_bind-2ycjA01 A:2-204                                                                                                                                                                                ----------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhh.eeeee.........hhhhhhhhhhhhhhhhhhh..hhh.eeee....hhhhhhhhhhhhhhhhhhhh.......eeeee.hhhhh...hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh.......hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ycj A  -7 GLVPRGSHMFIMIGERINGMFKDIREAILNKDPRPIQEWARRQAEKGAHYLDVNTGPTADDPVRVMEWLVKTIQEVVDLPCCLDSTNPDAIEAGLKVHRGHAMINSTSADQWKMDIFFPMAKKYEAAIIGLTMNEKGVPKDANDRSQLAMELVANADAHGIPMTELYIDPLILPVNVAQEHAVEVLETIRQIKLMANPAPRTVLGLSNVSQKCPDRPLINRTYLVMAMTAGLDAAIMDVDDDALVDAAATAHILLNKEIYCDSYLKTFRQK 263
                                     2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YCJ)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q3ACR9_CARHZ | Q3ACR9)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    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:0006760    folic acid-containing compound metabolic process    The chemical reactions and pathways involving a folic acid-containing compound, i.e. any of a group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more L-glutamic acid or L-glutamate units.
    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
        Q3ACR9_CARHZ | Q3ACR9: 2yci 2yck

(-) Related Entries Specified in the PDB File

2yci METHYLTRANSFERASE NATIVE
2yck METHYLTRANSFERASE BOUND WITH TETRAHYDROFOLATE
2ycl COMPLETE STRUCTURE OF THE CORRINOID,IRON-SULFUR PROTEIN INCLUDING THE N-TERMINAL DOMAIN WITH A 4FE-4S CLUSTER