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(-) Description

Title :  CRYSTAL STRUCTURE OF S-ADENOSYLMETHIONINE: 2-DIMETHYLMENAQUINONE METHYLTRANSFERASE (GK_1813) FROM GEOBACILLUS KAUSTOPHILUS HTA426
 
Authors :  J. Jeyakanthan, S. P. Kanaujia, Z. A. Rafi, K. Sekar, Y. Agari, A. Ebihar S. Kuramitsu, A. Shinkai, Y. Shiro, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  30 Mar 07  (Deposition) - 02 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Beta, Beta Alpha Domain, 2-Dimethylmenaquinone Methyltransferase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Jeyakanthan, S. P. Kanaujia, Z. A. Rafi, K. Sekar, Y. Agari, A. Ebihara, S. Kuramitsu, A. Shinkai, Y. Shiro, S. Yokoyama
Crystal Structure Of S-Adenosylmethionine:2-Dimethylmenaquinone Methyltransferas (Gk_1813) From Geobacillus Kaustophilus Hta426
To Be Published
PubMed: search

(-) Compounds

Molecule 1
    Chains: A
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL-21 CONDON PLUS (DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: GEOBACILLUS KAUSTOPHILUS
    Organism Taxid: 235909
    Strain: HTA426

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:45 , ALA A:72 , ARG A:77 , ARG A:97 , LYS A:118 , SER A:119 , LYS A:121 , HOH A:796BINDING SITE FOR RESIDUE ACT A 600

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Sequences/Alignments

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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:161
 aligned with Q5KYY8_GEOKA | Q5KYY8 from UniProtKB/TrEMBL  Length:161

    Alignment length:161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 
         Q5KYY8_GEOKA     1 MKTADLCDQFLDELQVCELPFQSYGGKRMFSGPIATVDVFEDNVLVREALETVPPGTVLVVDGKGSRRVALLGDRLAQIACERGLAGVIIHGCIRDSAEIGAMPIGVMAIGTCPVKSKKEGKGARDVVLEFGGVRWEPGAYVYADADGVVVANKDLLAKNG 161
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2pcnA00 A:3-163  [code=3.50.30.40, no name defined]                                                                                                               CATH domains
               Pfam domains Methyltransf_6-2pcnA01 A:3-153                                                                                                                         ---------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..eee.....ee......eeeeeeeee....hhhhhhhhhhh....eeeee.......eeehhhhhhhhhhh...eeeeeeee.hhhhhh....eeeeeee...........ee...eee..eee....eeeee..eeeee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pcn A   3 MKTADLCDQFLDELQVCELPFQSYGGKRMFSGPIATVDVFEDNVLVREALETVPPGTVLVVDGKGSRRVALLGDRLAQIACERGLAGVIIHGCIRDSAEIGAMPIGVMAIGTCPVKSKKEGKGARDVVLEFGGVRWEPGAYVYADADGVVVANKDLLAKNG 163
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2PCN)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: Methyltransf_6] (5)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q5KYY8_GEOKA | Q5KYY8)
molecular function
    GO:0047443    4-hydroxy-4-methyl-2-oxoglutarate aldolase activity    Catalysis of the reaction: 4-hydroxy-4-methyl-2-oxoglutarate = 2 pyruvate.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0008948    oxaloacetate decarboxylase activity    Catalysis of the reaction: oxaloacetate = pyruvate + CO2.
    GO:0008428    ribonuclease inhibitor activity    Stops, prevents or reduces the activity of a ribonuclease, any enzyme that catalyzes the hydrolysis of phosphodiester bonds in chains of RNA.
    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:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0043086    negative regulation of catalytic activity    Any process that stops or reduces the activity of an enzyme.
    GO:0051252    regulation of RNA metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA.

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