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(-) Description

Title :  METHIONINE GAMMA-LYASE (MGL) FROM TRICHOMONAS VAGINALIS
 
Authors :  G. Goodall, J. C. Mottram, G. H. Coombs, A. J. Lapthorn
Date :  25 Jul 00  (Deposition) - 19 Jul 01  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.18
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Methionine Biosynthesis, Plp-Dependent Enzymes, C-S Gamma Lyase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Goodall, J. C. Mottram, G. H. Coombs, A. J. Lapthorn
The Structure And Proposed Catalytic Mechanism Of Methionine Gamma-Lyase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - METHIONINE GAMMA-LYASE
    Cellular Location: CYTOPLASM
    Chains: A, B
    EC Number: 4.4.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE60
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MGL1
    Organism Scientific: TRICHOMONAS VAGINALIS
    Organism Taxid: 412133
    Strain: G3
    Synonym: MGL

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SO46Ligand/IonSULFATE ION
Biological Unit 1 (3, 18)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PLP4Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SO412Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:111 , ASN B:158 , LYS B:209 , VAL B:337 , SER B:338 , LEU B:339 , THR B:353 , ARG B:373 , PLP B:405BINDING SITE FOR RESIDUE SO4 B 406
2AC2SOFTWARETYR A:111 , ASN A:158 , LYS A:209 , VAL A:337 , SER A:338 , LEU A:339 , THR A:353 , ARG A:373 , PLP A:405 , HOH A:2327BINDING SITE FOR RESIDUE SO4 A 407
3AC3SOFTWAREHIS A:298 , LYS A:302 , TYR A:308BINDING SITE FOR RESIDUE SO4 A 408
4AC4SOFTWARELYS A:279 , LYS A:286 , HOH A:2260 , HOH A:2328BINDING SITE FOR RESIDUE SO4 A 409
5AC5SOFTWAREGLU B:177 , GLY B:178BINDING SITE FOR RESIDUE SO4 B 410
6AC6SOFTWAREGLU B:276 , LYS B:279 , PHE B:292 , GLU B:293 , ASP B:294BINDING SITE FOR RESIDUE SO4 B 411
7AC7SOFTWARESER A:85 , GLY A:86 , MET A:87 , TYR A:111 , ASN A:158 , ASP A:184 , THR A:186 , SER A:206 , THR A:208 , LYS A:209 , SO4 A:407 , TYR B:56 , ARG B:58BINDING SITE FOR RESIDUE PLP A 405
8AC8SOFTWARETYR A:56 , ARG A:58 , SER B:85 , GLY B:86 , MET B:87 , TYR B:111 , ASN B:158 , ASP B:184 , THR B:186 , SER B:206 , THR B:208 , LYS B:209 , SO4 B:406BINDING SITE FOR RESIDUE PLP B 405
9AC9SOFTWARETHR A:57 , ARG A:58 , LEU A:59 , GLY A:60 , ALA A:82 , ARG A:233 , SER A:243 , VAL A:244 , ILE A:245 , HOH A:2329BINDING SITE FOR RESIDUE GOL A 412

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1E5F)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Thr A:155 -Pro A:156
2Asn A:158 -Pro A:159
3Thr B:155 -Pro B:156
4Asn B:158 -Pro B:159

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1E5F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1E5F)

(-) Exons   (0, 0)

(no "Exon" information available for 1E5F)

(-) 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:393
 aligned with O15564_TRIVA | O15564 from UniProtKB/TrEMBL  Length:396

    Alignment length:393
                                    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       343       353       363       373       383       393   
         O15564_TRIVA     4 ERMTPATACIHANPQKDQFGAAIPPIYQTSTFVFDNCQQGGNRFAGQESGYIYTRLGNPTVSNLEGKIAFLEKTEACVATSSGMGAIAATVLTILKAGDHLISDECLYGCTHALFEHALTKFGIQVDFINTAIPGEVKKHMKPNTKIVYFETPANPTLKIIDMERVCKDAHSQEGVLVIADNTFCSPMITNPVDFGVDVVVHSATKYINGHTDVVAGLICGKADLLQQIRMVGIKDITGSVISPHDAWLITRGLSTLNIRMKAESENAMKVAEYLKSHPAVEKVYYPGFEDHEGHDIAKKQMRMSGSMITFILKSGFEGAKKLLDNLKLITLAVSLGGCESLIQHPASMTHAVVPKEEREAAGITDGMIRLSVGIEDADELIADFKQGLDALL 396
               SCOP domains d1e5fa_ A: Methionine gamma-lyase, MGL                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --1e5fA01 A:6-260 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                            1e5fA02 A:261-396 Aspartate Aminotransferase, domain 1                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh.......................hhhhhhhhhh............hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh..eeeee.....hhhhhhh...eeeeeee..........hhhhhhhhhhh....eeeee.........hhhhhh..eeeee.............eeeeehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhh.....eeeeee.hhhhhhhhhhhh...............eee..........hhhhhhhh.....eeeee....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e5f A   4 ERMTPATACIHANPQKDQFGAAIPPIYQTSTFVFDNCQQGGNRFAGQESGYIYTRLGNPTVSNLEGKIAFLEKTEACVATSSGMGAIAATVLTILKAGDHLISDECLYGCTHALFEHALTKFGIQVDFINTAIPGEVKKHMKPNTKIVYFETPANPTLKIIDMERVCKDAHSQEGVLVIADNTFCSPMITNPVDFGVDVVVHSATKYINGHTDVVAGLICGKADLLQQIRMVGIKDITGSVISPHDAWLITRGLSTLNIRMKAESENAMKVAEYLKSHPAVEKVYYPGFEDHEGHDIAKKQMRMYGSMITFILKSGFEGAKKLLDNLKLITLAVSLGGCESLIQHPASMTHAVVPKEEREAAGITDGMIRLSVGIEDADELIADFKQGLDALL 396
                                    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       343       353       363       373       383       393   


Chain B from PDB  Type:PROTEIN  Length:393
 aligned with O15564_TRIVA | O15564 from UniProtKB/TrEMBL  Length:396

    Alignment length:393
                                    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       343       353       363       373       383       393   
         O15564_TRIVA     4 ERMTPATACIHANPQKDQFGAAIPPIYQTSTFVFDNCQQGGNRFAGQESGYIYTRLGNPTVSNLEGKIAFLEKTEACVATSSGMGAIAATVLTILKAGDHLISDECLYGCTHALFEHALTKFGIQVDFINTAIPGEVKKHMKPNTKIVYFETPANPTLKIIDMERVCKDAHSQEGVLVIADNTFCSPMITNPVDFGVDVVVHSATKYINGHTDVVAGLICGKADLLQQIRMVGIKDITGSVISPHDAWLITRGLSTLNIRMKAESENAMKVAEYLKSHPAVEKVYYPGFEDHEGHDIAKKQMRMSGSMITFILKSGFEGAKKLLDNLKLITLAVSLGGCESLIQHPASMTHAVVPKEEREAAGITDGMIRLSVGIEDADELIADFKQGLDALL 396
               SCOP domains d1e5fb_ B: Methionine gamma-lyase, MGL                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --1e5fB01 B:6-260 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                            1e5fB02 B:261-396 Aspartate Aminotransferase, domain 1                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh.......................hhhhhhhhhh............hhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh..eeeee.....hhhhhhh...eeeeeee..........hhhhhhhhhh.....eeeee.........hhhhhh..eeeee.............eeeeehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhh.....eeeeee.hhhhhhhhhhhh...............eeee.........hhhhhhhh.....eeeee....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e5f B   4 ERMTPATACIHANPQKDQFGAAIPPIYQTSTFVFDNCQQGGNRFAGQESGYIYTRLGNPTVSNLEGKIAFLEKTEACVATSSGMGAIAATVLTILKAGDHLISDECLYGCTHALFEHALTKFGIQVDFINTAIPGEVKKHMKPNTKIVYFETPANPTLKIIDMERVCKDAHSQEGVLVIADNTFCSPMITNPVDFGVDVVVHSATKYINGHTDVVAGLICGKADLLQQIRMVGIKDITGSVISPHDAWLITRGLSTLNIRMKAESENAMKVAEYLKSHPAVEKVYYPGFEDHEGHDIAKKQMRMYGSMITFILKSGFEGAKKLLDNLKLITLAVSLGGCESLIQHPASMTHAVVPKEEREAAGITDGMIRLSVGIEDADELIADFKQGLDALL 396
                                    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       343       353       363       373       383       393
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1E5F)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O15564_TRIVA | O15564)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0018826    methionine gamma-lyase activity    Catalysis of the reaction: L-methionine = methanethiol + NH3 + 2-oxobutanoate.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.

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  O15564_TRIVA | O15564
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  4.4.1.11
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 Related Entries

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

UniProtKB/Swiss-Prot
        O15564_TRIVA | O15564: 1e5e

(-) Related Entries Specified in the PDB File

1e5e METHIONINE GAMMA-LYASE (MGL) FROM TRICHOMONAS VAGINALIS IN COMPLEX WITH PROPARGYLGLYCINE