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(-) Description

Title :  X-RAY STRUCTURE OF A C-3'-METHYLTRANSFERASE IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE AND SUGAR PRODUCT
 
Authors :  N. A. Bruender, J. B. Thoden, M. Kaur, M. K. Avey, H. M. Holden
Date :  07 Jun 10  (Deposition) - 30 Jun 10  (Release) - 23 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  S-Adenosyl-L-Homocysteine, Kijanose, Tetronitrose, Tetradeoxy Sugar, Keto Sugar, Micromonospora Chalcea, Tcab9, C-3'-Methyltransferase, Sugar Methylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. A. Bruender, J. B. Thoden, M. Kaur, M. K. Avey, H. M. Holden
Molecular Architecture Of A C-3'-Methyltransferase Involved In The Biosynthesis Of D-Tetronitrose.
Biochemistry V. 49 5891 2010
PubMed-ID: 20527922  |  Reference-DOI: 10.1021/BI100782B

(-) Compounds

Molecule 1 - METHYLTRANSFERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: ROSETTA2 DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASIMD
    Gene: TCAB9
    Organism Scientific: MICROMONOSPORA CHALCEA
    Organism Taxid: 1874

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric/Biological Unit (4, 4)
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)
2PO41Ligand/IonPHOSPHATE ION
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
4ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE 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:418 , HOH A:454 , HOH A:499 , HOH A:505 , HOH A:512BINDING SITE FOR RESIDUE SAH A 415
2AC2SOFTWARECYS A:13 , CYS A:16 , CYS A:54 , CYS A:57BINDING SITE FOR RESIDUE ZN A 416
3AC3SOFTWAREPRO A:67 , ARG A:68 , HOH A:455 , HOH A:514BINDING SITE FOR RESIDUE PO4 A 417
4AC4SOFTWARETYR 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 , SAH A:415 , HOH A:461 , HOH A:468 , HOH A:479 , HOH A:504BINDING SITE FOR RESIDUE JHZ A 418

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NDJ)

(-) 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 3NDJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NDJ)

(-) Exons   (0, 0)

(no "Exon" information available for 3NDJ)

(-) 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 ---Methyltransf_13-3ndjA02 A:13-73                              -----------Methyltransf_23-3ndjA01 A:85-248                                                                                                                                    --Methyltransf_14-3ndjA03 A:251-409                                                                                                                              ----- Pfam domains
         Sec.struct. author ..........eeeeeeeeeee...............eeeeeeeee.....eee....hhhhhh......hhhhhhhhhhhhhhhhhhhhhh.......eeeee......hhhhhhhh..eeeee..hhhhhhhhhh....ee....hhhhhhhhhhhhh.eeeeeee.hhhhh.hhhhhhhhhhhheeeeeeeeeeeehhhhhhhhhhhhhh.....ee.hhhhhhhhhhh..eeeeeeeeehhhh.eeeeeeee......hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhh........eee.hhhhh.ee......eeee.hhh......eeee.hhhhhhhhhhhhhhhhhh..eeee.....ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ndj A  10 PTACRVCGGGVQEFLDLGRQPLSDRFRKPDELDDEFTYRLAVGRCDSCEMVQLTEEVPRDLMFHEVYPYHSSGSSVMREHFAMLARDFLATELTGPDPFIVEIGCNDGIMLRTIQEAGVRHLGFEPSSGVAAKAREKGIRVRTDFFEKATADDVRRTEGPANVIYAANTLCHIPYVQSVLEGVDALLAPDGVFVFEDPYLGDIVAKTSFDQIYDEHFFLFSATSVQGMAQRCGFELVDVQRLPVHGGEVRYTLARQGSRTPSAAVAQLLAAEREQELSDMATLRAFAGNVVKIRDELTALLHRLRAEGRSVVGYGATAKSATVTNFCGIGPDLVHSVYDTTPDKQNRLTPGAHIPVRPASAFSDPYPDYALLFAWNHAEEIMAKEQEFHQAGGRWILYVPEVHIR 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)
  - → 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  (0, 0)

(no "SCOP Domain" information available for 3NDJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NDJ)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: no clan defined [family: Methyltransf_13] (2)
(-)
Clan: no clan defined [family: Methyltransf_14] (2)

(-) 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 | B5L6K6: 3ndi 4e2w 4e2x 4e2y 4e2z 4e30 4e31 4e32 4e33

(-) Related Entries Specified in the PDB File

3ndi THE SAME PROTEIN COMPLEXED WITH S-ADENOSYLMETHIONINE AND DTMP