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(-) Description

Title :  X-RAY STRUCTURE OF THE C-3'-METHYLTRANSFERASE TCAB9 IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE AND REDUCED DTDP-SUGAR SUBSTRATE
 
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 :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Kijanose, Tetronitrose, Tetradeoxy 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
    Chains: A
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: ROSETTA2 DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TCAB9
    Organism Scientific: MICROMONOSPORA CHALCEA
    Organism Taxid: 1874
    Synonym: C-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
10N21Ligand/Ion(2R,4S,5R,6R)-4-AMINO-5-HYDROXY-6-METHYLTETRAHYDRO-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
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 , HOH A:614 , HOH A:658 , HOH A:663 , HOH A:670BINDING SITE FOR RESIDUE SAH A 502
3AC3SOFTWARETYR A:76 , TYR A:78 , ASN A:177 , HIS A:181 , TYR A:222 , GLU A:224 , HIS A:225 , HIS A:254 , GLY A:324 , 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 , HOH A:621 , HOH A:628 , HOH A:639 , HOH A:662BINDING SITE FOR RESIDUE 0N2 A 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E33)

(-) 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 4E33)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E33)

(-) Exons   (0, 0)

(no "Exon" information available for 4E33)

(-) 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:404
 aligned with B5L6K6_MICCH | B5L6K6 from UniProtKB/TrEMBL  Length:414

    Alignment length:404
                                    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       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410    
         B5L6K6_MICCH    11 TACRVCGGGVQEFLDLGRQPLSDRFRKPDELDDEFTYRLAVGRCDSCEMVQLTEEVPRDLMFHEVYPYHSSGSSVMREHFAMLARDFLATELTGPDPFIVEIGCNDGIMLRTIQEAGVRHLGFEPSSGVAAKAREKGIRVRTDFFEKATADDVRRTEGPANVIYAANTLCHIPYVQSVLEGVDALLAPDGVFVFEDPYLGDIVAKTSFDQIYDEHFFLFSATSVQGMAQRCGFELVDVQRLPVHGGEVRYTLARQGSRTPSAAVAQLLAAEREQELSDMATLRAFAGNVVKIRDELTALLHRLRAEGRSVVGYGATAKSATVTNFCGIGPDLVHSVYDTTPDKQNRLTPGAHIPVRPASAFSDPYPDYALLFAWNHAEEIMAKEQEFHQAGGRWILYVPEVHIR 414
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeee...............eeeeeeeee.....eee....hhhhhh......hhhhhhhhhhhhhhhhhhhhhh.......eeeee......hhhhhhhh..eeeee..hhhhhhhhhhh...ee....hhhhhhhhhhhhh.eeeeeee.hhhhh.hhhhhhhhhhhheeeeeeeeeeeehhhhhhhhhhhhhh.....ee.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
                 4e33 A  11 TACRVCGGGVQEFLDLGRQPLSDRFRKPDELDDEFTYRLAVGRCDSCEMVQLTEEVPRDLMFHEVYPYHSSGSSVMREHFAMLARDFLATELTGPDPFIVEIGCNDGIMLRTIQEAGVRHLGFEPSSGVAAKAREKGIRVRTDFFEKATADDVRRTEGPANVIYAANTLCHIPYVQSVLEGVDALLAPDGVFVFEDPYLGDIVAKTSFDQIYDEHFFLFSATSVQGMAQRCGFELVDVQRLPVHGGEVRYTLARQGSRTPSAAVAQLLAAEREQELSDMATLRAFAGNVVKIRDELTALLHRLRAEGRSVVGYGATAKSATVTNFCGIGPDLVHSVYDTTPDKQNRLTPGAHIPVRPASAFSDPYPDYALLFAWNHAEEIMAKEQEFHQAGGRWILYVPEVHIR 414
                                    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       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410
   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 4E33)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E33)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E33)

(-) 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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  4e33
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 Related Entries

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

UniProtKB/TrEMBL
        B5L6K6_MICCH | B5L6K6: 3ndi 3ndj 4e2w 4e2x 4e2y 4e2z 4e30 4e31 4e32

(-) Related Entries Specified in the PDB File

4e2w H181N MUTANT C-3'-METHYLTRANSFERASE TCAB9
4e2x Y222F MUTANT C-3'-METHYLTRANSFERASE TCAB9
4e2y E224Q 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