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(-) Description

Title :  CRYSTAL 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 :  02 May 13  (Deposition) - 07 May 14  (Release) - 25 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
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, 27)

Asymmetric/Biological Unit (6, 27)
No.NameCountTypeFull Name
156D2Ligand/Ion(3R)-2-OXO-3-PHENYLBUTANOIC ACID
2CA5Ligand/IonCALCIUM ION
3FE2Ligand/IonFE (III) ION
4HF22Ligand/Ion(2R)-2-HYDROXY-3-PHENYLPROPANOIC ACID
5MSE14Mod. Amino AcidSELENOMETHIONINE
6SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
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 , MSE A:240 , MSE A:241 , 56D A:402 , HOH A:506 , HOH A:523 , HOH A:566 , HOH A:569 , HOH A:585 , HOH A:670 , HOH A:673BINDING SITE FOR RESIDUE SAH A 401
02AC2SOFTWARETRP A:99 , ARG A:127 , CYS A:136 , MSE A:240 , HIS A:243 , ASP A:272 , PHE A:287 , PHE A:291 , HIS A:295 , SAH A:401 , FE A:403 , HOH A:646 , HOH A:647BINDING SITE FOR RESIDUE 56D A 402
03AC3SOFTWAREHIS A:243 , HIS A:295 , 56D A:402 , HOH A:646 , HOH A:647BINDING SITE FOR RESIDUE FE A 403
04AC4SOFTWAREASP A:309 , PHE A:312 , CYS A:319 , LYS A:322 , LYS B:322 , ALA B:324 , HOH B:612BINDING SITE FOR RESIDUE HF2 A 404
05AC5SOFTWAREASP A:217BINDING SITE FOR RESIDUE CA A 405
06AC6SOFTWAREPHE A:180 , PRO A:181 , GLY A:182BINDING SITE FOR RESIDUE CA A 406
07AC7SOFTWAREGLU A:106 , ARG A:127 , HOH A:795BINDING SITE FOR RESIDUE CA A 407
08AC8SOFTWARECYS B:136 , GLY B:166 , GLY B:168 , ARG B:172 , ASP B:189 , ILE B:190 , GLY B:216 , ASP B:217 , ALA B:218 , ARG B:219 , PHE B:239 , MSE B:240 , MSE B:241 , ASP B:244 , 56D B:402 , HOH B:521 , HOH B:544 , HOH B:568 , HOH B:573 , HOH B:665 , HOH B:671 , HOH B:744BINDING SITE FOR RESIDUE SAH B 401
09AC9SOFTWARETRP B:99 , ARG B:127 , CYS B:136 , MSE B:240 , HIS B:243 , ASP B:272 , PHE B:287 , PHE B:291 , HIS B:295 , SAH B:401 , FE B:403 , HOH B:643 , HOH B:644BINDING SITE FOR RESIDUE 56D B 402
10BC1SOFTWAREHIS B:243 , HIS B:295 , 56D B:402 , HOH B:643 , HOH B:644BINDING SITE FOR RESIDUE FE B 403
11BC2SOFTWARELYS A:322 , ALA A:324 , ASP B:309 , PHE B:312 , CYS B:319 , LYS B:321 , LYS B:322 , PHE B:334 , HOH B:809BINDING SITE FOR RESIDUE HF2 B 404
12BC3SOFTWAREASP A:309 , HOH A:703 , HOH A:704 , ASP B:306 , ASP B:309 , HOH B:612BINDING SITE FOR RESIDUE CA B 405
13BC4SOFTWARELYS B:44BINDING SITE FOR RESIDUE CA B 406

(-) SS Bonds  (0, 0)

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

(-) 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 4KIB)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KIB)

(-) 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:333
                                                                                                                                                                                                                                                                                                                                                                             
               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.hhhhhhhh.eeeee.hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.....hhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhh.eeeeeeee....eeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kib A   5 VSEAQARRAVADIFNSTLASSAIGAAWELGALDELRENGKLDVSDFAVRHDLHEPAVVGmFTALASVGIVRREGATVVVGPYFDEANHHRSLFHWLNQGSGELFRRmPQVLPNENRTGKFYQRDAGAISYACREISERYFDPAFWAAVDGLGYTPTTVADLGSGSGERLIQIARRFPGVRGLGVDIADGAIAmAEKEVAAKGFGDQISFVRGDARTIDQVSARGEFAEVDLLTCFmmGHDFWPRENCVQTLRKLRAAFPNVRRFLLGDATRTVGIPDRELPVFTLGFEFGHDmmGVYLPTLDEWDGVFEEGGWRCVKKHAIDSLSVSVVFELE 337
                                    14        24        34        44        54        64        74        84        94       104      |114       124       134       144       154       164       174       184       194  |    204       214       224       234     ||244       254       264       274       284       294  ||   304       314       324       334   
                                                                                      64-MSE                                        111-MSE                                                                               197-MSE                                    240-MSE                                                  297-MSE                                    
                                                                                                                                                                                                                                                                      241-MSE                                                  298-MSE                                   


Chain B from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeehhhhhhhh..hhhhhhhhhhhhhhh..eeee..eeee..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh.....eeeee.hhhhhhhh.hhhhhhhh.eeeee.hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.....hhhhh..hhhhhhhhhhhhh....hhhhhhh........eeeeee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kib B   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     
                                                                                        64-MSE                                        111-MSE                                                                               197-MSE                                    240-MSE                                                  297-MSE                                    
                                                                                                                                                                                                                                                                        241-MSE                                                  298-MSE
   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 4KIB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

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

(-) Related Entries Specified in the PDB File

4kic 4kif 4kig 4m6x 4m6y 4m71 4m72 4m73 4m74