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(-) Description

Title :  METHYLTRANSFERASE BOUND WITH TETRAHYDROFOLATE
 
Authors :  S. Goetzl, J. -H. Jeoung, S. E. Hennig, H. Dobbek
Date :  16 Mar 11  (Deposition) - 08 Jun 11  (Release) - 16 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  X
Biol. Unit 1:  X  (2x)
Keywords :  Transferase, Tim-Barrel, Vitamin B12 (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: X
    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

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO47Ligand/IonSULFATE ION
3THG1Ligand/Ion(6S)-5,6,7,8-TETRAHYDROFOLATE
Biological Unit 1 (3, 18)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO414Ligand/IonSULFATE ION
3THG2Ligand/Ion(6S)-5,6,7,8-TETRAHYDROFOLATE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER X:-1 , HIS X:0 , MET X:1 , HOH X:2117BINDING SITE FOR RESIDUE SO4 X1264
2AC2SOFTWAREHIS X:0 , ARG X:193 , HOH X:2118BINDING SITE FOR RESIDUE SO4 X1265
3AC3SOFTWAREARG X:91 , GLY X:92BINDING SITE FOR RESIDUE SO4 X1266
4AC4SOFTWAREARG X:8 , TRP X:31 , HOH X:2119BINDING SITE FOR RESIDUE SO4 X1267
5AC5SOFTWAREASP X:232 , ASP X:233 , ASP X:234 , ALA X:235 , HOH X:2098BINDING SITE FOR RESIDUE SO4 X1268
6AC6SOFTWAREALA X:51 , ASP X:52 , ASP X:53 , PRO X:54BINDING SITE FOR RESIDUE SO4 X1269
7AC7SOFTWARETRP X:104 , HOH X:2120BINDING SITE FOR RESIDUE SO4 X1270
8AC8SOFTWAREGLY X:92 , HIS X:93BINDING SITE FOR RESIDUE GOL X1271
9AC9SOFTWAREMET X:12 , PHE X:13 , ASP X:76 , ASN X:97 , LEU X:123 , ASP X:161 , GLY X:197 , SER X:199 , ASN X:200 , GLN X:203 , LYS X:204 , ARG X:208 , ILE X:228 , HOH X:2008 , HOH X:2009 , HOH X:2060 , HOH X:2124 , HOH X:2125 , HOH X:2126 , HOH X:2127BINDING SITE FOR RESIDUE THG X7216

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly X:-8 -Gly X:-7
2Asn X:97 -Ser X:98
3Asn X:189 -Pro X:190

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YCK)

(-) 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 X from PDB  Type:PROTEIN  Length:272
 aligned with Q3ACR9_CARHZ | Q3ACR9 from UniProtKB/TrEMBL  Length:263

    Alignment length:272
                                     1                                                                                                                                                                                                                                                                      
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261  
         Q3ACR9_CARHZ     - ---------MFIMIGERINGMFKDIREAILNKDPRPIQEWARRQAEKGAHYLDVNTGPTADDPVRVMEWLVKTIQEVVDLPCCLDSTNPDAIEAGLKVHRGHAMINSTSADQWKMDIFFPMAKKYEAAIIGLTMNEKGVPKDANDRSQLAMELVANADAHGIPMTELYIDPLILPVNVAQEHAVEVLETIRQIKLMANPAPRTVLGLSNVSQKCPDRPLINRTYLVMAMTAGLDAAIMDVDDDALVDAAATAHILLNKEIYCDSYLKTFRQK 263
               SCOP domains d2yckx_ X: automated matches                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------Pterin_bind-2yckX01 X:2-204                                                                                                                                                                                ----------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee......hhhhhhhhhh.hhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhh.eeeee.........hhhhhhhhhhhhhhhhhhh..hhh.eeee....hhhhhhhhhhhhhhhhhhhh.......eeeee.hhhhh...hhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh.......hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yck X  -8 GGLVPRGSHMFIMIGERINGMFKDIREAILNKDPRPIQEWARRQAEKGAHYLDVNTGPTADDPVRVMEWLVKTIQEVVDLPCCLDSTNPDAIEAGLKVHRGHAMINSTSADQWKMDIFFPMAKKYEAAIIGLTMNEKGVPKDANDRSQLAMELVANADAHGIPMTELYIDPLILPVNVAQEHAVEVLETIRQIKLMANPAPRTVLGLSNVSQKCPDRPLINRTYLVMAMTAGLDAAIMDVDDDALVDAAATAHILLNKEIYCDSYLKTFRQK 263
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261
   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, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain X   (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 2ycj

(-) Related Entries Specified in the PDB File

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