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(-) Description

Title :  MUTANT STRUCTURE OF METHYLTRANSFERASE FROM STREPTOMYCES HYGROSCOPICUS COMPLEXED WITH S-ADENOSYL-L-HOMOCYSTEINE AND METHYLPHENYLPYRUVIC ACID
 
Authors :  Y. C. Liu, X. W. Zou, H. C. Chan, C. J. Huang, T. L. Li
Date :  12 Aug 13  (Deposition) - 25 Jun 14  (Release) - 25 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Methyltransferase, Sam/Ppy Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. W. Zou, Y. C. Liu, N. S. Hsu, C. J. Huang, S. Y. Lyu, H. C. Chan, C. Y. Chang, H. W. Yeh, K. H. Lin, C. J. Wu, M. D. Tsai, T. L. Li
Structure And Mechanism Of A Nonhaem-Iron Sam-Dependent C-Methyltransferase And Its Engineering To A Hydratase And An O-Methyltransferase
Acta Crystallogr. , Sect. D V. 70 1549 2014
PubMed-ID: 24914966  |  Reference-DOI: 10.1107/S1399004714005239

(-) Compounds

Molecule 1 - METHYLTRANSFERASE MPPJ
    Chains: A, B
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MPPJ
    Mutation: YES
    Organism Scientific: STREPTOMYCES HYGROSCOPICUS
    Organism Taxid: 1912

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 14)

Asymmetric/Biological Unit (6, 14)
No.NameCountTypeFull Name
156D2Ligand/Ion(3R)-2-OXO-3-PHENYLBUTANOIC ACID
2CA4Ligand/IonCALCIUM ION
3FE2Ligand/IonFE (III) ION
4HF22Ligand/Ion(2R)-2-HYDROXY-3-PHENYLPROPANOIC ACID
5OXY2Ligand/IonOXYGEN MOLECULE
6SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:140 , GLY A:166 , GLY A:168 , ARG A:172 , ASP A:189 , ILE A:190 , ALA A:191 , GLY A:216 , ASP A:217 , ALA A:218 , ARG A:219 , PHE A:239 , MET A:240 , MET A:241 , LEU A:244 , HOH A:516 , HOH A:695BINDING SITE FOR RESIDUE SAH A 401
02AC2SOFTWARETRP A:99 , ARG A:127 , CYS A:136 , MET A:240 , HIS A:243 , ASP A:272 , ALA A:273 , PHE A:287 , PHE A:291 , HIS A:295 , FE A:403 , OXY A:408BINDING SITE FOR RESIDUE 56D A 402
03AC3SOFTWAREHIS A:243 , HIS A:295 , 56D A:402 , OXY A:408BINDING SITE FOR RESIDUE FE A 403
04AC4SOFTWAREASP A:309 , PHE A:312 , CYS A:319 , VAL A:320 , LYS A:321 , LYS A:322 , LYS B:322 , ALA B:324BINDING SITE FOR RESIDUE HF2 A 404
05AC5SOFTWAREASP A:306 , ASP A:309 , ASP B:306 , CA B:405BINDING SITE FOR RESIDUE CA A 406
06AC6SOFTWARESER A:225 , GLY A:228 , HOH A:703BINDING SITE FOR RESIDUE CA A 407
07AC7SOFTWARELEU A:244 , 56D A:402 , FE A:403BINDING SITE FOR RESIDUE OXY A 408
08AC8SOFTWARESER B:140 , GLY B:166 , GLY B:168 , ARG B:172 , ASP B:189 , ILE B:190 , ALA B:191 , GLY B:216 , ASP B:217 , ALA B:218 , ARG B:219 , PHE B:239 , MET B:240 , LEU B:244BINDING SITE FOR RESIDUE SAH B 401
09AC9SOFTWARETRP B:99 , ARG B:127 , CYS B:136 , MET B:240 , HIS B:243 , ASP B:272 , PHE B:287 , PHE B:291 , HIS B:295 , FE B:403 , OXY B:406BINDING SITE FOR RESIDUE 56D B 402
10BC1SOFTWAREHIS B:243 , HIS B:295 , 56D B:402 , OXY B:406BINDING SITE FOR RESIDUE FE B 403
11BC2SOFTWARELYS A:322 , ALA A:324 , ASP B:309 , PHE B:312 , CYS B:319 , LYS B:322 , CA B:405 , HOH B:587BINDING SITE FOR RESIDUE HF2 B 404
12BC3SOFTWAREASP A:309 , CA A:406 , ASP B:306 , ASP B:309 , HF2 B:404BINDING SITE FOR RESIDUE CA B 405
13BC4SOFTWARELEU B:244 , 56D B:402 , FE B:403 , HOH B:620BINDING SITE FOR RESIDUE OXY B 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M6Y)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:246 -Pro A:247
2Trp B:246 -Pro B:247

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M6Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M6Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4M6Y)

(-) 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:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeehhhhhhhhh.hhhhhhhhhhhhhh...eeee..eeee..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.....hhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhh.eeeeeee.....eeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m6y A   3 TEVSEAQARRAVADIFNSTLASSAIGAAWELGALDELRENGKLDVSDFAVRHDLHEPAVVGMFTALASVGIVRREGATVVVGPYFDEANHHRSLFHWLNQGSGELFRRMPQVLPNENRTGKFYQRDAGAISYACREISERYFDPAFWAAVDGLGYTPTTVADLGSGSGERLIQIARRFPGVRGLGVDIADGAIAMAEKEVAAKGFGDQISFVRGDARTIDQVSARGEFAEVDLLTCFMMGHLFWPRENCVQTLRKLRAAFPNVRRFLLGDATRTVGIPDRELPVFTLGFEFGHDMMGVYLPTLDEWDGVFEEGGWRCVKKHAIDSLSVSVVFELE 337
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332     


Chain B from PDB  Type:PROTEIN  Length:339
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeehhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhh...eeeee..hhhhhhhhhhhhhh............hhhhh....hhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.....hhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhh.eeeeeee.....eeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m6y B  -1 SHMSTEVSEAQARRAVADIFNSTLASSAIGAAWELGALDELRENGKLDVSDFAVRHDLHEPAVVGMFTALASVGIVRREGATVVVGPYFDEANHHRSLFHWLNQGSGELFRRMPQVLPNENRTGKFYQRDAGAISYACREISERYFDPAFWAAVDGLGYTPTTVADLGSGSGERLIQIARRFPGVRGLGVDIADGAIAMAEKEVAAKGFGDQISFVRGDARTIDQVSARGEFAEVDLLTCFMMGHLFWPRENCVQTLRKLRAAFPNVRRFLLGDATRTVGIPDRELPVFTLGFEFGHDMMGVYLPTLDEWDGVFEEGGWRCVKKHAIDSLSVSVVFELE 337
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328
   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 4M6Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M6Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M6Y)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        MPPJ_STRHY | Q643C8: 4kib 4kic 4kif 4kig 4m6x 4m71 4m72 4m73 4m74

(-) Related Entries Specified in the PDB File

4kib WILD TYPE PROTEIN
4kic
4kif
4kig
4m6x
4m71
4m72
4m73
4m74