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(-) Description

Title :  X-RAY STRUCTURE OF THE E224Q MUTANT OF TCAB9, A C-3'-METHYLTRANSFERASE, IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE AND SUGAR PRODUCT
 
Authors :  N. A. Bruender, H. M. Holden
Date :  09 Mar 12  (Deposition) - 25 Apr 12  (Release) - 30 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Kijanose, Tetronitrose, Tetradeoxy Sugar, Keto Sugar, Sugar Methylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. A. Bruender, H. M. Holden
Probing The Catalytic Mechanism Of A C-3'-Methyltransferase Involved In The Biosynthesis Of D-Tetronitrose.
Protein Sci. V. 21 876 2012
PubMed-ID: 22495991  |  Reference-DOI: 10.1002/PRO.2074

(-) Compounds

Molecule 1 - TCAB9
    ChainsA
    EC Number2.1.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28
    Expression System StrainROSETTA2 DE3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneTCAB9
    MutationYES
    Organism ScientificMICROMONOSPORA CHALCEA
    Organism Taxid1874
    SynonymC-3'-METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1JHZ1Ligand/Ion(2R,4S,6R)-4-AMINO-4,6-DIMETHYL-5-OXOTETRAHYDRO-2H-PYRAN-2-YL [(2R,3S,5R)-3-HYDROXY-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE (NON-PREFERRED NAME)
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:13 , CYS A:16 , CYS A:54 , CYS A:57BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWAREPHE A:72 , TYR A:76 , SER A:80 , PHE A:90 , ILE A:112 , GLY A:113 , ASN A:115 , PHE A:133 , GLU A:134 , PRO A:135 , SER A:136 , PHE A:154 , PHE A:155 , ALA A:176 , ASN A:177 , THR A:178 , ILE A:182 , TYR A:184 , JHZ A:503 , HOH A:642 , HOH A:652 , HOH A:671 , HOH A:672BINDING SITE FOR RESIDUE SAH A 502
3AC3SOFTWARETYR A:76 , TYR A:78 , HIS A:181 , TYR A:222 , GLN A:224 , HIS A:225 , HIS A:254 , THR A:326 , ALA A:327 , LYS A:328 , ASP A:348 , THR A:349 , THR A:350 , LYS A:353 , ASN A:385 , HIS A:386 , GLU A:389 , ILE A:390 , LYS A:393 , SAH A:502 , HOH A:621 , HOH A:690 , HOH A:693 , HOH A:739BINDING SITE FOR RESIDUE JHZ A 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E2Y)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asp A:373 -Pro A:374
2Val A:408 -Pro A:409

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E2Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E2Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4E2Y)

(-) 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:405
 aligned with B5L6K6_MICCH | B5L6K6 from UniProtKB/TrEMBL  Length:414

    Alignment length:405
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409     
         B5L6K6_MICCH    10 PTACRVCGGGVQEFLDLGRQPLSDRFRKPDELDDEFTYRLAVGRCDSCEMVQLTEEVPRDLMFHEVYPYHSSGSSVMREHFAMLARDFLATELTGPDPFIVEIGCNDGIMLRTIQEAGVRHLGFEPSSGVAAKAREKGIRVRTDFFEKATADDVRRTEGPANVIYAANTLCHIPYVQSVLEGVDALLAPDGVFVFEDPYLGDIVAKTSFDQIYDEHFFLFSATSVQGMAQRCGFELVDVQRLPVHGGEVRYTLARQGSRTPSAAVAQLLAAEREQELSDMATLRAFAGNVVKIRDELTALLHRLRAEGRSVVGYGATAKSATVTNFCGIGPDLVHSVYDTTPDKQNRLTPGAHIPVRPASAFSDPYPDYALLFAWNHAEEIMAKEQEFHQAGGRWILYVPEVHIR 414
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeeeeeeeee...............eeeeeeeee.....eee....hhhhhh......hhhhhhhhhhhhhhhhhhhhhh.......eeeee......hhhhhhhh..eeeee..hhhhhhhhhh....ee....hhhhhhhhhhhhh.eeeeeee.hhhhh.hhhhhhhhhhhheeeeeeeeeeeehhhhhhhhhhhhhh........hhhhhhhhhhhh.eeeeeeeeehhhh.eeeeeeee......hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh........eee.hhhhh.ee......eeee.hhh......eeee.hhhhhhhhhhhhhhhhhh..eeee.....ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e2y A  10 PTACRVCGGGVQEFLDLGRQPLSDRFRKPDELDDEFTYRLAVGRCDSCEMVQLTEEVPRDLMFHEVYPYHSSGSSVMREHFAMLARDFLATELTGPDPFIVEIGCNDGIMLRTIQEAGVRHLGFEPSSGVAAKAREKGIRVRTDFFEKATADDVRRTEGPANVIYAANTLCHIPYVQSVLEGVDALLAPDGVFVFEDPYLGDIVAKTSFDQIYDQHFFLFSATSVQGMAQRCGFELVDVQRLPVHGGEVRYTLARQGSRTPSAAVAQLLAAEREQELSDMATLRAFAGNVVKIRDELTALLHRLRAEGRSVVGYGATAKSATVTNFCGIGPDLVHSVYDTTPDKQNRLTPGAHIPVRPASAFSDPYPDYALLFAWNHAEEIMAKEQEFHQAGGRWILYVPEVHIR 414
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409     

   Legend:   → Mismatch (orange background)
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  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 4E2Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E2Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E2Y)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (B5L6K6_MICCH | B5L6K6)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    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: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.

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 Related Entries

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

UniProtKB/TrEMBL
        B5L6K6_MICCH | B5L6K63ndi 3ndj 4e2w 4e2x 4e2z 4e30 4e31 4e32 4e33

(-) Related Entries Specified in the PDB File

4e2w H181N MUTANT C-3'-METHYLTRANSFERASE TCAB9
4e2x Y222F MUTANT C-3'-METHYLTRANSFERASE TCAB9
4e2z H225N MUTANT C-3'-METHYLTRANSFERASE TCAB9
4e30 H181N/E224Q DOUBLE MUTANT C-3'-METHYLTRANSFERASE TCAB9
4e31 Y76F MUTANT C-3'-METHYLTRANSFERASE TCAB9
4e32 WILD-TYPE C-3'-METHYLTRANSFERASE TCAB9 COMPLEXED WITH SAH AND DTDP-SUGAR SUBSTRATE
4e33 WILD-TYPE C-3'-METHYLTRANSFERASE TCAB9 COMPLEXED WITH SAH AND REDUCED DTDP-SUGAR SUBSTRATE