Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF METHYLTRANSFERASE FROM STREPTOMYCES HYGROSCOPICUS COMPLEXED WITH 4-HYDROXYPHENYLPYRUVIC 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 :  2.40
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, 15)

Asymmetric/Biological Unit (4, 15)
No.NameCountTypeFull Name
134H2Ligand/Ion(2R)-2-HYDROXY-3-(4-HYDROXYPHENYL)PROPANOIC ACID
2CA9Ligand/IonCALCIUM ION
3ENO2Ligand/Ion3-(4-HYDROXY-PHENYL)PYRUVIC ACID
4FE2Ligand/IonFE (III) ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:99 , ARG A:127 , PHE A:144 , MET A:240 , HIS A:243 , ASP A:272 , ALA A:273 , PHE A:287 , PHE A:291 , HIS A:295 , LEU A:328 , FE A:502 , HOH A:602BINDING SITE FOR RESIDUE ENO A 501
02AC2SOFTWAREHIS A:243 , HIS A:295 , ENO A:501 , HOH A:601 , HOH A:602BINDING SITE FOR RESIDUE FE A 502
03AC3SOFTWAREASP A:309 , PHE A:312 , CYS A:319 , LYS A:322 , HOH A:609 , LYS B:322 , HIS B:323 , ALA B:324 , VAL B:332 , 34H B:503BINDING SITE FOR RESIDUE 34H A 503
04AC4SOFTWAREHOH B:668BINDING SITE FOR RESIDUE CA A 504
05AC5SOFTWAREARG A:109 , GLU B:106 , HOH B:678BINDING SITE FOR RESIDUE CA A 505
06AC6SOFTWAREASP A:306 , ASP A:309 , ASP B:306 , ASP B:309BINDING SITE FOR RESIDUE CA A 507
07AC7SOFTWARETRP B:99 , ARG B:127 , PHE B:144 , MET B:240 , HIS B:243 , ASP B:272 , ALA B:273 , PHE B:287 , PHE B:291 , HIS B:295 , LEU B:328 , FE B:502 , HOH B:602 , HOH B:603BINDING SITE FOR RESIDUE ENO B 501
08AC8SOFTWAREHIS B:243 , HIS B:295 , ENO B:501 , HOH B:602 , HOH B:603BINDING SITE FOR RESIDUE FE B 502
09AC9SOFTWARELYS A:322 , HIS A:323 , ALA A:324 , VAL A:332 , 34H A:503 , ASP B:309 , PHE B:312 , CYS B:319 , LYS B:321 , LYS B:322 , HOH B:653BINDING SITE FOR RESIDUE 34H B 503
10BC1SOFTWAREGLU A:106 , ARG A:127 , ARG B:109 , HOH B:640BINDING SITE FOR RESIDUE CA B 504
11BC2SOFTWARELYS B:44BINDING SITE FOR RESIDUE CA B 505
12BC3SOFTWAREPHE B:180 , GLY B:182BINDING SITE FOR RESIDUE CA B 506
13BC4SOFTWAREARG B:248BINDING SITE FOR RESIDUE CA B 507

(-) SS Bonds  (0, 0)

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

(-) 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 4KIG)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KIG)

(-) 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:332
                                                                                                                                                                                                                                                                                                                                                                            
               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.hhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.....hhhhh..hhhhhhhhhhhhh....hhhhhhh.......eeeeeee.....eeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kig A   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  


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.hhhhhhhhhhhhh.......eeeee.hhhhh....hhhhhhhh.eeeee.hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.....hhhhh..hhhhhhhhhhhhh....hhhhhhh.......eeeeeee.....eeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kig 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)
  - → 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 4KIG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    34H  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ENO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:326 - Ser A:327   [ RasMol ]  
    Trp A:246 - Pro A:247   [ RasMol ]  
    Trp B:246 - Pro B:247   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4kig
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MPPJ_STRHY | Q643C8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  MPPJ_STRHY | Q643C8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MPPJ_STRHY | Q643C8: 4kib 4kic 4kif 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.
4kif THE SAME PROTEIN COMPLEXED WITH PPY.
4m6x
4m6y
4m71
4m72
4m73
4m74