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(-) Description

Title :  ENGINEERED EGTD VARIANT EGTD-M252V,E282A IN COMPLEX WITH TRYPTOPHAN AND SAH
 
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 :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (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
    ChainsA, B, C, D
    EC Number2.1.1.44
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET19M
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneEGTD, MSMEG_6247, MSMEI_6086
    MutationYES
    Organism ScientificMYCOBACTERIUM SMEGMATIS
    Organism Taxid1772
    StrainATCC 607
    SynonymHISTIDINE-ALPHA-N-METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MG2Ligand/IonMAGNESIUM ION
3SAH4Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
4TRP4Mod. Amino AcidTRYPTOPHAN
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
4TRP1Mod. Amino AcidTRYPTOPHAN
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
4TRP1Mod. Amino AcidTRYPTOPHAN
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
4TRP1Mod. Amino AcidTRYPTOPHAN
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
4TRP1Mod. Amino AcidTRYPTOPHAN

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:39 , PHE A:47 , TYR A:56 , GLY A:161 , ASN A:166 , TYR A:206 , ALA A:282 , SER A:284 , HOH A:633 , HOH A:743binding site for residue TRP A 401
02AC2SOFTWARELYS A:36 , TYR A:39 , GLU A:84 , GLY A:86 , SER A:87 , THR A:89 , LYS A:92 , ASP A:113 , VAL A:114 , GLY A:140 , ASP A:141 , PHE A:142 , LEU A:160 , GLY A:161 , HOH A:635 , HOH A:640 , HOH A:642 , HOH A:649 , HOH A:690 , HOH A:693 , HOH A:699binding site for residue SAH A 402
03AC3SOFTWARETYR B:39 , TYR B:56 , GLY B:161 , ASN B:166 , TYR B:206 , ALA B:282 , SER B:284 , HOH B:741 , HOH B:745 , HOH B:756binding site for residue TRP B 401
04AC4SOFTWARELYS B:36 , TYR B:39 , PHE B:47 , GLY B:86 , SER B:87 , LYS B:92 , ASP B:113 , VAL B:114 , GLY B:140 , ASP B:141 , PHE B:142 , LEU B:160 , GLY B:161 , HOH B:623 , HOH B:629 , HOH B:657 , HOH B:665 , HOH B:683 , HOH B:703 , HOH B:720 , HOH B:757binding site for residue SAH B 402
05AC5SOFTWAREHOH B:522 , HOH B:539 , HOH B:553 , HOH C:529 , HOH C:546 , HOH C:577binding site for residue MG B 403
06AC6SOFTWAREGLY C:-1 , HIS C:0 , HOH C:592 , HIS D:305binding site for residue CL C 401
07AC7SOFTWAREPHE C:47 , TYR C:56 , GLY C:161 , THR C:163 , ASN C:166 , TYR C:206 , PHE C:216 , ALA C:282 , SER C:284 , HOH C:750 , HOH C:805binding site for residue TRP C 402
08AC8SOFTWARELYS C:36 , TYR C:39 , PHE C:47 , GLY C:86 , SER C:87 , GLY C:88 , LYS C:92 , ASP C:113 , VAL C:114 , GLY C:140 , ASP C:141 , PHE C:142 , GLY C:161 , THR C:163 , HOH C:634 , HOH C:647 , HOH C:658 , HOH C:662 , HOH C:710 , HOH C:822binding site for residue SAH C 403
09AC9SOFTWAREHOH B:524 , HOH B:542 , HOH B:583 , HOH C:531 , HOH C:572 , HOH D:520binding site for residue MG C 404
10AD1SOFTWAREPHE D:38 , PHE D:47 , TYR D:56 , GLY D:161 , THR D:163 , ASN D:166 , TYR D:206 , THR D:213 , ALA D:282 , SER D:284 , HOH D:633binding site for residue TRP D 401
11AD2SOFTWARETYR D:39 , PHE D:47 , GLY D:86 , SER D:87 , GLY D:88 , LYS D:92 , ASP D:113 , VAL D:114 , GLY D:140 , ASP D:141 , PHE D:142 , GLY D:161 , THR D:163 , HOH D:649 , HOH D:657 , HOH D:669 , HOH D:673 , HOH D:710 , HOH D:797binding site for residue SAH D 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PIP)

(-) 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:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh...ee..ee.....hhhhh.....eeeee..hhhhhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhh.....hhhhhhhhhhhhhhhhhhh...hhh.eeeeeeee....eeeeeeee...eeeeehhhheeeee....eeeeeeee..hhhhhhhhhhhh..eeeeeee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pip A   3 LSLANYLAAAAEALRRDVRAGLTATQKSLPPKWFYDAVGSDLFDQITRLPEYYPTRTEAQILRTRSAEIISAAGADTLVELGSGTSEKTRMLLDAMRDAELLRRFIPFDVDAGVLRSAGAAIGAEYPGIEIDAVCGDFEEHLGKIPHVGRRLVVFLGSTIGNLTPAPRAEFLSTLADTLQPGDSLLLGTDLVKDTGRLVRAYDDAAGVTAAFNRNVLAVVNRELSADFDLDAFEHVAKWNSDEERIEVWLRARTAQHVRVAALDLEVDFAAGEEMLTAVSCKFRPENVVAELAEAGLRQTHWWTDPAGDFGLSLAVW 401
                                    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     ||
                                   11|                                                                                                                                                                                                                                                                                                               320|
                                    14                                                                                                                                                                                                                                                                                                                401

Chain B from PDB  Type:PROTEIN  Length:310
                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh...ee..ee.....hhhhh.....eeeee..hhhhhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhh.....hhhhhhhhhhhhhhhhhhh...hhh.eeeeeeee....eeeeeeee...eeeeehhhheeeee....eeeeeeee..hhhhhhhhhhhh..eeeeeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pip B  13 SAAEALRRDVRAGLTATQKSLPPKWFYDAVGSDLFDQITRLPEYYPTRTEAQILRTRSAEIISAAGADTLVELGSGTSEKTRMLLDAMRDAELLRRFIPFDVDAGVLRSAGAAIGAEYPGIEIDAVCGDFEEHLGKIPHVGRRLVVFLGSTIGNLTPAPRAEFLSTLADTLQPGDSLLLGTDLVKDTGRLVRAYDDAAGVTAAFNRNVLAVVNRELSADFDLDAFEHVAKWNSDEERIEVWLRARTAQHVRVAALDLEVDFAAGEEMLTAVSCKFRPENVVAELAEAGLRQTHWWTDPAGDFGLSLAVRW 401
                                    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       401
                                                                                                                                                                                                                                                                                                                                              321|
                                                                                                                                                                                                                                                                                                                                               401

Chain C from PDB  Type:PROTEIN  Length:315
                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh...ee..ee.....hhhhh.....eeeee..hhhhhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhh....hhhhhhhhhhhhhhhhhhh...hhh.eeeeeeee....eeeeeeee...eeeeehhhheeeee....eeeeeeee..hhhhhhhhhhhh..eeeeeee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pip C  -1 GHMALSLAAEALRRDVRAGLTATQKSLPPKWFYDAVGSDLFDQITRLPEYYPTRTEAQILRTRSAEIISAAGADTLVELGSGTSEKTRMLLDAMRDAELLRRFIPFDVDAGVLRSAGAAIGAEYPGIEIDAVCGDFEEHLGKIPHVGRRLVVFLGSTIGNLTPAPRAEFLSTLADTLQPGDSLLLGTDLVKDTGRLVRAYDDAAGVTAAFNRNVLAVVNRELSADFDLDAFEHVAKWNSDEERIEVWLRARTAQHVRVAALDLEVDFAAGEEMLTAVSCKFRPENVVAELAEAGLRQTHWWTDPAGDFGLSLAVR 321
                                  ||16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316     
                                  5|                                                                                                                                                                                                                                                                                                                   
                                  14                                                                                                                                                                                                                                                                                                                   

Chain D from PDB  Type:PROTEIN  Length:319
                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh...ee.eee.....hhhhh.....eeeee..hhhhhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhh....hhhhhhhhhhhhhhhhhhh...hhh.eeeeeeee....eeeeeeee...eeeee....eeeee....eeeeeeee..hhhhhhhhhhhh..eeeeeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pip D   4 SLANYLAADSAAEALRRDVRAGLTATQKSLPPKWFYDAVGSDLFDQITRLPEYYPTRTEAQILRTRSAEIISAAGADTLVELGSGTSEKTRMLLDAMRDAELLRRFIPFDVDAGVLRSAGAAIGAEYPGIEIDAVCGDFEEHLGKIPHVGRRLVVFLGSTIGNLTPAPRAEFLSTLADTLQPGDSLLLGTDLVKDTGRLVRAYDDAAGVTAAFNRNVLAVVNRELSADFDLDAFEHVAKWNSDEERIEVWLRARTAQHVRVAALDLEVDFAAGEEMLTAVSCKFRPENVVAELAEAGLRQTHWWTDPAGDFGLSLAVRW 401
                                    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       ||
                                                                                                                                                                                                                                                                                                                                                       321|
                                                                                                                                                                                                                                                                                                                                                        401

   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 4PIP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        EGTD_MYCS2 | A0R5M84pim 4pin 4pio 4uy5 4uy6 4uy7

(-) Related Entries Specified in the PDB File

4pim EGTD WT, APO FORM
4pin EGTD WT IN COMPLEX WITH N,N-DIMETHYLHISTIDINE
4pio EGTD WT IN COMPLEX WITH N,N-DIMETHYLHISTIDINE AND SAH