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(-) Description

Title :  CRYSTAL STRUCTURE OF METHYLTRANSFERASE FROM STREPTOMYCES HYGROSCOPICUS COMPLEXED WITH S-ADENOSYL-L-METHIONINE AND 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 :  2.43
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  (6, 22)

Asymmetric/Biological Unit (6, 22)
No.NameCountTypeFull Name
1CA13Ligand/IonCALCIUM ION
2FE2Ligand/IonFE (III) ION
3HF22Ligand/Ion(2R)-2-HYDROXY-3-PHENYLPROPANOIC ACID
4IOD1Ligand/IonIODIDE ION
5PPY2Ligand/Ion3-PHENYLPYRUVIC ACID
6SAM2Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:136 , 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 , ASP A:244 , PPY A:402 , HOH A:521 , HOH A:522 , HOH A:525 , HOH A:538 , HOH A:544 , HOH A:562 , HOH A:575BINDING SITE FOR RESIDUE SAM A 401
02AC2SOFTWARETRP A:99 , ARG A:127 , MET A:240 , HIS A:243 , ASP A:272 , ALA A:273 , PHE A:287 , PHE A:291 , HIS A:295 , SAM A:401 , FE A:403 , HOH A:501 , HOH A:502BINDING SITE FOR RESIDUE PPY A 402
03AC3SOFTWAREHIS A:243 , HIS A:295 , PPY A:402 , HOH A:501 , HOH A:502BINDING SITE FOR RESIDUE FE A 403
04AC4SOFTWAREASP A:309 , PHE A:312 , CYS A:319 , LYS A:322 , PHE A:334 , LYS B:322 , ALA B:324BINDING SITE FOR RESIDUE HF2 A 404
05AC5SOFTWAREARG A:12BINDING SITE FOR RESIDUE CA A 405
06AC6SOFTWAREARG A:75BINDING SITE FOR RESIDUE CA A 406
07AC7SOFTWAREGLU A:106 , ARG A:127 , HOH A:651 , ARG B:109BINDING SITE FOR RESIDUE CA A 407
08AC8SOFTWAREARG A:109 , ARG B:127BINDING SITE FOR RESIDUE CA A 408
09AC9SOFTWAREASP A:217 , HOH A:644BINDING SITE FOR RESIDUE CA A 409
10BC1SOFTWAREGLN A:113BINDING SITE FOR RESIDUE CA A 410
11BC2SOFTWARELYS A:123BINDING SITE FOR RESIDUE CA A 411
12BC3SOFTWARELYS A:44BINDING SITE FOR RESIDUE IOD A 412
13BC4SOFTWARECYS B:136 , GLY B:166 , 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 , MET B:241 , ASP B:244 , PPY B:402 , HOH B:513 , HOH B:522 , HOH B:524 , HOH B:538 , HOH B:560 , HOH B:589 , HOH B:612BINDING SITE FOR RESIDUE SAM B 401
14BC5SOFTWARETRP B:99 , ARG B:127 , MET B:240 , HIS B:243 , ALA B:273 , PHE B:287 , PHE B:291 , HIS B:295 , SAM B:401 , FE B:403 , HOH B:501 , HOH B:502BINDING SITE FOR RESIDUE PPY B 402
15BC6SOFTWAREHIS B:243 , HIS B:295 , PPY B:402 , HOH B:501 , HOH B:502BINDING SITE FOR RESIDUE FE B 403
16BC7SOFTWARELYS A:322 , ALA A:324 , ASP B:309 , CYS B:319 , LYS B:322 , PHE B:334BINDING SITE FOR RESIDUE HF2 B 404
17BC8SOFTWAREARG B:75BINDING SITE FOR RESIDUE CA B 405
18BC9SOFTWAREARG B:12BINDING SITE FOR RESIDUE CA B 406
19CC1SOFTWAREGLN B:113BINDING SITE FOR RESIDUE CA B 408
20CC2SOFTWAREASP B:217BINDING SITE FOR RESIDUE CA B 409
21CC3SOFTWARETHR B:220 , ASP B:222 , GLN B:223BINDING SITE FOR RESIDUE CA B 410

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Glu A:4 -Val A:5
2Trp A:246 -Pro A:247
3Trp B:246 -Pro B:247

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KIC)

(-) 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:334
                                                                                                                                                                                                                                                                                                                                                                              
               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.hhhhhhhh....hhhhh.eeeee.hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.....hhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhh..eeeeeeee....eeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kic A   4 EVSEAQARRAVADIFNSTLASSAIGAAWELGALDELRENGKLDVSDFAVRHDLHEPAVVGMFTALASVGIVRREGATVVVGPYFDEANHHRSLFHWLNQGSGELFRRMPQVLPNENRTGKFYQRDAGAISYACREISERYFDPAFWAAVDGLGYTPTTVADLGSGSGERLIQIARRFPGVRGLGVDIADGAIAMAEKEVAAKGFGDQISFVRGDARTIDQVSARGEFAEVDLLTCFMMGHDFWPRENCVQTLRKLRAAFPNVRRFLLGDATRTVGIPDRELPVFTLGFEFGHDMMGVYLPTLDEWDGVFEEGGWRCVKKHAIDSLSVSVVFELE 337
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333    


Chain B from PDB  Type:PROTEIN  Length:332
                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeehhhhhhhh..hhhhhhhhhhhhhh...eeee..eeee..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh....eeeee.hhhhhhhh..hhhhhhh.eeeee.hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.....hhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhh..eeeeeeee....eeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kic B   6 SEAQARRAVADIFNSTLASSAIGAAWELGALDELRENGKLDVSDFAVRHDLHEPAVVGMFTALASVGIVRREGATVVVGPYFDEANHHRSLFHWLNQGSGELFRRMPQVLPNENRTGKFYQRDAGAISYACREISERYFDPAFWAAVDGLGYTPTTVADLGSGSGERLIQIARRFPGVRGLGVDIADGAIAMAEKEVAAKGFGDQISFVRGDARTIDQVSARGEFAEVDLLTCFMMGHDFWPRENCVQTLRKLRAAFPNVRRFLLGDATRTVGIPDRELPVFTLGFEFGHDMMGVYLPTLDEWDGVFEEGGWRCVKKHAIDSLSVSVVFELE 337
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335
   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 4KIC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4kif 4kig 4m6x 4m6y 4m71 4m72 4m73 4m74

(-) Related Entries Specified in the PDB File

4kib THE SAME PROTEIN COMPLEXED WITH SAM AND PPY
4kif
4kig
4m6x
4m6y
4m71
4m72
4m73
4m74