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(-) Description

Title :  ERGOTHIONEINE-BIOSYNTHETIC METHYLTRANSFERASE EGTD IN COMPLEX WITH N,N-DIMETHYLHISTIDINE
 
Authors :  A. Vit, F. P. Seebeck, W. Blankenfeldt
Date :  09 May 14  (Deposition) - 03 Dec 14  (Release) - 07 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Methyltransferase, Ergothioneine, Histidine Betaine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Vit, L. Misson, W. Blankenfeldt, F. P. Seebeck
Ergothioneine Biosynthetic Methyltransferase Egtd Reveals The Structural Basis Of Aromatic Amino Acid Betaine Biosynthesis.
Chembiochem V. 16 119 2015
PubMed-ID: 25404173  |  Reference-DOI: 10.1002/CBIC.201402522
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HISTIDINE-SPECIFIC METHYLTRANSFERASE EGTD
    Chains: A, B
    EC Number: 2.1.1.44
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET19M
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: EGTD, MSMEG_6247, MSMEI_6086
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM SMEGMATIS
    Organism Taxid: 1772
    Strain: ATCC 607
    Synonym: HISTIDINE-ALPHA-N-METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1AVI2Ligand/IonN,N-DIMETHYL-L-HISTIDINE
2PO45Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1AVI1Ligand/IonN,N-DIMETHYL-L-HISTIDINE
2PO43Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1AVI1Ligand/IonN,N-DIMETHYL-L-HISTIDINE
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:39 , PHE A:47 , TYR A:56 , GLY A:161 , THR A:163 , ASN A:166 , TYR A:206 , GLU A:282 , SER A:284 , HOH A:601 , HOH A:631binding site for residue AVI A 401
2AC2SOFTWAREHOH A:508 , GLU B:72 , SER B:75 , ALA B:76 , HIS B:305 , PO4 B:402binding site for residue PO4 A 402
3AC3SOFTWAREARG A:19 , ARG A:23binding site for residue PO4 A 403
4AC4SOFTWAREASP A:233 , ASP A:235 , ALA A:236 , HOH A:700 , HOH A:799 , HOH A:833binding site for residue PO4 A 404
5AC5SOFTWARETYR B:39 , TYR B:56 , GLY B:161 , ASN B:166 , TYR B:206 , GLU B:282 , SER B:284 , HOH B:582 , HOH B:623binding site for residue AVI B 401
6AC6SOFTWARETYR A:8 , LYS A:148 , PO4 A:402 , HOH B:501binding site for residue PO4 B 402
7AC7SOFTWAREASP B:80 , ARG B:107 , ARG B:108 , GLY B:153binding site for residue PO4 B 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PIN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PIN)

(-) Sequences/Alignments

Asymmetric 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:320
                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh...eeeeee.....hhhhh.....eeeee..hhhhhhhhhhhhhhhhhhhhh.....eeeeeee...hhhhhhhh.....hhhhhhhhhhhhhhhhhhh...hhh.eeeeeeee....eeeeeeee...eeeeehhhheeeee....eeeeeeee..hhhhhhhhhhhh..eeeeeee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pin A   0 HMALSLANYLAADSAAEALRRDVRAGLTATQKSLPPKWFYDAVGSDLFDQITRLPEYYPTRTEAQILRTRSAEIISAAGADTLVELGSSEKTRMLLDAMRDAELLRRFIPFDVDAGVLRSAGAAIGAEYPGIEIDAVCGDFEEHLGKIPHVGRRLVVFLGSTIGNLTPAPRAEFLSTLADTLQPGDSLLLGTDLVKDTGRLVRAYDDAAGVTAAFNRNVLAVVNRELSADFDLDAFEHVAKWNSDEERIEMWLRARTAQHVRVAALDLEVDFAAGEEMLTEVSCKFRPENVVAELAEAGLRQTHWWTDPAGDFGLSLAVR 321
                                     9        19        29        39        49        59        69        79       |91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321
                                                                                                                  87|                                                                                                                                                                                                                                       
                                                                                                                   90                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:321
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh...eeeeee.....hhhhh.....eeeee..hhhhhhhhhhhhhhhhhhhhh.....eeeeeee...hhhhhhhhh....hhhhhhhhhhhhhhhhhhh...hhh.eeeeeeee....eeeeeeee...eeeeehhhheeeee....eeeeeeee..hhhhhhhhhhhhh.eeeeeee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pin B  -1 GHMALSLANYLAADSAAEALRRDVRAGLTATQKSLPPKWFYDAVGSDLFDQITRLPEYYPTRTEAQILRTRSAEIISAAGADTLVELGSSEKTRMLLDAMRDAELLRRFIPFDVDAGVLRSAGAAIGAEYPGIEIDAVCGDFEEHLGKIPHVGRRLVVFLGSTIGNLTPAPRAEFLSTLADTLQPGDSLLLGTDLVKDTGRLVRAYDDAAGVTAAFNRNVLAVVNRELSADFDLDAFEHVAKWNSDEERIEMWLRARTAQHVRVAALDLEVDFAAGEEMLTEVSCKFRPENVVAELAEAGLRQTHWWTDPAGDFGLSLAVR 321
                                     8        18        28        38        48        58        68        78        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320 
                                                                                                                   87|                                                                                                                                                                                                                                       
                                                                                                                    90
   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 4PIN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

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 Related Entries

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

UniProtKB/Swiss-Prot
        EGTD_MYCS2 | A0R5M8: 4pim 4pio 4pip 4uy5 4uy6 4uy7

(-) Related Entries Specified in the PDB File

4pim EGTD, APO FORM
4pio EGTD IN COMPLEX WITH N,N-DIMETHYLHISTIDINE AND SAH
4pip EGTD DOUBLE MUTANT (M252V, E282A) HYOA IN COMPLEX WITH TRYPTOPHAN AND SAH