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(-) Description

Title :  CRYSTAL STRUCTURE OF METHYLTRANSFERASE FROM STREPTOMYCES HYGROSCOPICUS COMPLEXED WITH PHENYLPYRUVIC ACID
 
Authors :  Y. C. Liu, X. W. Zou, H. C. Chan, C. J. Huang, T. L. Li
Date :  02 May 13  (Deposition) - 07 May 14  (Release) - 25 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Methyltransferase, Sam Binding 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
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MPPJ
    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  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2FE2Ligand/IonFE (III) ION
3HF22Ligand/Ion(2R)-2-HYDROXY-3-PHENYLPROPANOIC ACID
4PPY3Ligand/Ion3-PHENYLPYRUVIC ACID

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:99 , ARG A:127 , HIS A:243 , ASP A:272 , PHE A:287 , PHE A:291 , HIS A:295 , FE A:502 , HOH A:601 , HOH A:739 , HOH A:774BINDING SITE FOR RESIDUE PPY A 501
02AC2SOFTWAREHIS A:243 , HIS A:295 , PPY A:501 , HOH A:601 , HOH A:739BINDING SITE FOR RESIDUE FE A 502
03AC3SOFTWAREASP A:309 , PHE A:312 , CYS A:319 , VAL A:320 , LYS A:321 , LYS A:322 , HOH A:727 , LYS B:322 , HF2 B:503BINDING SITE FOR RESIDUE HF2 A 503
04AC4SOFTWARELYS A:205 , GLY A:206 , PHE A:207 , ASP A:209 , GLN A:210 , HIS B:0 , MET B:1 , GLU B:283BINDING SITE FOR RESIDUE PPY A 504
05AC5SOFTWAREGLU A:106 , ARG A:127 , HOH A:790 , ARG B:109BINDING SITE FOR RESIDUE CA A 505
06AC6SOFTWAREASP A:306 , ASP A:309 , HOH A:784 , ASP B:306 , ASP B:309BINDING SITE FOR RESIDUE CA A 506
07AC7SOFTWARETRP B:99 , ARG B:127 , HIS B:243 , ASP B:272 , PHE B:287 , PHE B:291 , HIS B:295 , FE B:502 , HOH B:601 , HOH B:602 , HOH B:658BINDING SITE FOR RESIDUE PPY B 501
08AC8SOFTWAREHIS B:243 , HIS B:295 , PPY B:501 , HOH B:601 , HOH B:602BINDING SITE FOR RESIDUE FE B 502
09AC9SOFTWARELYS A:322 , ALA A:324 , HF2 A:503 , ASP B:309 , PHE B:312 , CYS B:319 , LYS B:321 , LYS B:322 , HOH B:655BINDING SITE FOR RESIDUE HF2 B 503
10BC1SOFTWARESER B:-1 , HIS B:0 , SER B:2BINDING SITE FOR RESIDUE CA B 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Trp A:246 -Pro A:247
2Asp A:326 -Ser A:327
3Trp B:246 -Pro B:247

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KIF)

(-) 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..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh.....eeeee.hhhhhhhh.hhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.....hhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhh.eeeeeee.....eeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kif A   3 TEVSEAQARRAVADIFNSTLASSAIGAAWELGALDELRENGKLDVSDFAVRHDLHEPAVVGMFTALASVGIVRREGATVVVGPYFDEANHHRSLFHWLNQGSGELFRRMPQVLPNENRTGKFYQRDAGAISYACREISERYFDPAFWAAVDGLGYTPTTVADLGSGSGERLIQIARRFPGVRGLGVDIADGAIAMAEKEVAAKGFGDQISFVRGDARTIDQVSARGEFAEVDLLTCFMMGHDFWPRENCVQTLRKLRAAFPNVRRFLLGDATRTVGIPDRELPVFTLGFEFGHDMMGVYLPTLDEWDGVFEEGGWRCVKKHAIDSLSVSVVFELE 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 .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeehhhhhhhh..hhhhhhhhhhhhhh...eeee..eeee..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh.....eeeee.hhhhh..hhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.....hhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhh.eeeeeee.....eeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kif B  -1 SHMSTEVSEAQARRAVADIFNSTLASSAIGAAWELGALDELRENGKLDVSDFAVRHDLHEPAVVGMFTALASVGIVRREGATVVVGPYFDEANHHRSLFHWLNQGSGELFRRMPQVLPNENRTGKFYQRDAGAISYACREISERYFDPAFWAAVDGLGYTPTTVADLGSGSGERLIQIARRFPGVRGLGVDIADGAIAMAEKEVAAKGFGDQISFVRGDARTIDQVSARGEFAEVDLLTCFMMGHDFWPRENCVQTLRKLRAAFPNVRRFLLGDATRTVGIPDRELPVFTLGFEFGHDMMGVYLPTLDEWDGVFEEGGWRCVKKHAIDSLSVSVVFELE 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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    → 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 4KIF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:326 - Ser A:327   [ RasMol ]  
    Trp A:246 - Pro A:247   [ RasMol ]  
    Trp B:246 - Pro B:247   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        MPPJ_STRHY | Q643C8: 4kib 4kic 4kig 4m6x 4m6y 4m71 4m72 4m73 4m74

(-) Related Entries Specified in the PDB File

4kib THE SAME PROTEIN COMPLEXED WITH SAH AND MEPPY.
4kic THE SAME PROTEIN COMPLEXED WITH SAM AND PPY.
4kig
4m6x
4m6y
4m71
4m72
4m73
4m74