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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PYRIDOXAL-5'-PHOSPHATE DEPENDENT L-METHIONINE GAMMA-LYASE FROM PSEUDOMONAS PUTIDA
 
Authors :  H. Motoshima, K. Inagaki, T. Kumasaka, M. Furuichi, H. Inoue, T. Tamura, N. Esaki, K. Soda, N. Tanaka, M. Yamamoto, H. Tanaka
Date :  06 Jul 00  (Deposition) - 08 May 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Pyridoxal-5'-Phosphate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Motoshima, K. Inagaki, T. Kumasaka, M. Furuichi, H. Inoue, T. Tamura, N. Esaki, K. Soda, N. Tanaka, M. Yamamoto, H. Tanaka
Crystal Structure Of The Pyridoxal 5'-Phosphate Dependent L-Methionine Gamma-Lyase From Pseudomonas Putida
J. Biochem. (Tokyo) V. 128 349 2000
PubMed-ID: 10965031
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METHIONINE GAMMA-LYASE
    Chains: A, B, C, D
    EC Number: 4.4.1.11
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1LLP4Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)

(-) Sites  (0, 0)

(no "Site" information available for 1GC0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1GC0)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Ser A:158 -Pro A:159
2Tyr A:291 -Pro A:292
3Ser B:158 -Pro B:159
4Asn B:161 -Pro B:162
5Tyr B:291 -Pro B:292
6Ser C:158 -Pro C:159
7Asn C:161 -Pro C:162
8Tyr C:291 -Pro C:292
9Ser D:158 -Pro D:159
10Tyr D:291 -Pro D:292

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GC0)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYS_MET_METAB_PPPS00868 Cys/Met metabolism enzymes pyridoxal-phosphate attachment site.MEGL_PSEPU203-217
 
 
 		  4A:203-217
B:203-217
C:203-217
D:203-217

(-) Exons   (0, 0)

(no "Exon" information available for 1GC0)

(-) 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:355
 aligned with MEGL_PSEPU | P13254 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:392
                                    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       326       336       346       356       366       376       386       396  
           MEGL_PSEPU     7 LPGFATRAIHHGYDPQDHGGALVPPVYQTATFTFPTVEYGAACFAGEQAGHFYSRISNPTLNLLEARMASLEGGEAGLALASGMGAITSTLWTLLRPGDEVLLGNTLYGCTFAFLHHGIGEFGVKLRHVDMADLQALEAAMTPATRVIYFESPANPNMHMADIAGVAKIARKHGATVVVDNTYCTPYLQRPLELGADLVVHSATKYLSGHGDITAGIVVGSQALVDRIRLQGLKDMTGAVLSPHDAALLMRGIKTLNLRMDRHCANAQVLAEFLARQPQVELIHYPGLASFPQYTLARQQMSQPGGMIAFELKGGIGAGRRFMNALQLFSRAVSLGDAESLAQHPASMTHSSYTPEERAHYGISEGLVRLSVGLEDIDDLLADVQQALKASA 398
               SCOP domains d1gc0a_ A: Methionine gamma-lyase,                      MGL                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -1gc0A01 A:8-262 Type I PLP-depende                     nt aspartate aminotransferase-like (Major domain)                                                                                                                                                       1gc0A02 A:263-395 Aspartate Am                inotransferase, domain 1                                                               --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh..hhhhhh................---------------------.hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh.eeeee...hhhhhhhhh...eeeeeee..........hhhhhhhhhhhhh.eeeee...hhhhhhhhhhhh..eeeee.............eeeeehhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.----------------....eeeeee.hhhhhhhhhhhhh...ee.........eeehhhhh.....hhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYS_MET_METAB_P------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gc0 A   7 LPGFATRAIHHGYDPQDHGGALVPPVYQTATFTFP---------------------SNPTLNLLEARMASLEGGEAGLALASGMGAITSTLWTLLRPGDEVLLGNTLYGCTFAFLHHGIGEFGVKLRHVDMADLQALEAAMTPATRVIYFESPANPNMHMADIAGVAKIARKHGATVVVDNTYCTPYLQRPLELGADLVVHSATkYLSGHGDITAGIVVGSQALVDRIRLQGLKDMTGAVLSPHDAALLMRGIKTLNLRMDRHCANAQVLAEFLARQPQVELIHYP----------------QPGGMIAFELKGGIGAGRRFMNALQLFSRAVSLGDAESLAQHPASMTHSSYTPEERAHYGISEGLVRLSVGLEDIDDLLADVQQALKASA 398
                                    16        26        36    |    -         -      | 66        76        86        96       106       116       126       136       146       156       166       176       186       196       206    |  216       226       236       246       256       266       276       286     |   -         -  |    316       326       336       346       356       366       376       386       396  
                                                             41                    63                                                                                                                                                 211-LLP                                                                          292              309                                                                                         


Chain B from PDB  Type:PROTEIN  Length:357
 aligned with MEGL_PSEPU | P13254 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:392
                                    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       326       336       346       356       366       376       386       396  
           MEGL_PSEPU     7 LPGFATRAIHHGYDPQDHGGALVPPVYQTATFTFPTVEYGAACFAGEQAGHFYSRISNPTLNLLEARMASLEGGEAGLALASGMGAITSTLWTLLRPGDEVLLGNTLYGCTFAFLHHGIGEFGVKLRHVDMADLQALEAAMTPATRVIYFESPANPNMHMADIAGVAKIARKHGATVVVDNTYCTPYLQRPLELGADLVVHSATKYLSGHGDITAGIVVGSQALVDRIRLQGLKDMTGAVLSPHDAALLMRGIKTLNLRMDRHCANAQVLAEFLARQPQVELIHYPGLASFPQYTLARQQMSQPGGMIAFELKGGIGAGRRFMNALQLFSRAVSLGDAESLAQHPASMTHSSYTPEERAHYGISEGLVRLSVGLEDIDDLLADVQQALKASA 398
               SCOP domains d1gc0b_ B: Methionine gamma-lyase, MGL                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -1gc0B01 B:8-262 Type I PLP-dependent                   aspartate aminotransferase-like (Major domain)                                                                                                                                                          1gc0B02 B:263-395 Aspartate Am                 inotransferase, domain 1                                                              --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh..hhhhhh...................------------------.hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhh.eeeee...hhhhhhhhh...eeeeeee..........hhhhhhhhhh....eeeee...hhhhhhhhhhhh..eeeee.............eeeeehhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.-----------------...eeeeee.hhhhhhhhhhhhh...ee.........eeehhhhh.....hhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYS_MET_METAB_P------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gc0 B   7 LPGFATRAIHHGYDPQDHGGALVPPVYQTATFTFPTVE------------------SNPTLNLLEARMASLEGGEAGLALASGMGAITSTLWTLLRPGDEVLLGNTLYGCTFAFLHHGIGEFGVKLRHVDMADLQALEAAMTPATRVIYFESPANPNMHMADIAGVAKIARKHGATVVVDNTYCTPYLQRPLELGADLVVHSATkYLSGHGDITAGIVVGSQALVDRIRLQGLKDMTGAVLSPHDAALLMRGIKTLNLRMDRHCANAQVLAEFLARQPQVELIHYP-----------------PGGMIAFELKGGIGAGRRFMNALQLFSRAVSLGDAESLAQHPASMTHSSYTPEERAHYGISEGLVRLSVGLEDIDDLLADVQQALKASA 398
                                    16        26        36       | -         -      | 66        76        86        96       106       116       126       136       146       156       166       176       186       196       206    |  216       226       236       246       256       266       276       286     |   -         -   |   316       326       336       346       356       366       376       386       396  
                                                                44                 63                                                                                                                                                 211-LLP                                                                          292               310                                                                                        


Chain C from PDB  Type:PROTEIN  Length:363
 aligned with MEGL_PSEPU | P13254 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:392
                                    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       326       336       346       356       366       376       386       396  
           MEGL_PSEPU     7 LPGFATRAIHHGYDPQDHGGALVPPVYQTATFTFPTVEYGAACFAGEQAGHFYSRISNPTLNLLEARMASLEGGEAGLALASGMGAITSTLWTLLRPGDEVLLGNTLYGCTFAFLHHGIGEFGVKLRHVDMADLQALEAAMTPATRVIYFESPANPNMHMADIAGVAKIARKHGATVVVDNTYCTPYLQRPLELGADLVVHSATKYLSGHGDITAGIVVGSQALVDRIRLQGLKDMTGAVLSPHDAALLMRGIKTLNLRMDRHCANAQVLAEFLARQPQVELIHYPGLASFPQYTLARQQMSQPGGMIAFELKGGIGAGRRFMNALQLFSRAVSLGDAESLAQHPASMTHSSYTPEERAHYGISEGLVRLSVGLEDIDDLLADVQQALKASA 398
               SCOP domains d1gc0c_ C: Methionine gamma-lyase, M                    GL                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -1gc0C01 C:8-262 Type I PLP-dependen                    t aspartate aminotransferase-like (Major domain)                                                                                                                                                        1gc0C02 C:263-395 Aspartate Aminot         ransferase, domain 1                                                                      --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh..hhhhhh.................--------------------.hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh..eeeee...hhhhhhhhh...eeeeeee..........hhhhhhhhhhhhh.eeeee...hhhhhhhhhhhh..eeeee.............eeeeehhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.....---------.......eeeeee.hhhhhhhhhhhhh...ee.........eeehhhhh.....hhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYS_MET_METAB_P------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gc0 C   7 LPGFATRAIHHGYDPQDHGGALVPPVYQTATFTFPT--------------------SNPTLNLLEARMASLEGGEAGLALASGMGAITSTLWTLLRPGDEVLLGNTLYGCTFAFLHHGIGEFGVKLRHVDMADLQALEAAMTPATRVIYFESPANPNMHMADIAGVAKIARKHGATVVVDNTYCTPYLQRPLELGADLVVHSATkYLSGHGDITAGIVVGSQALVDRIRLQGLKDMTGAVLSPHDAALLMRGIKTLNLRMDRHCANAQVLAEFLARQPQVELIHYPGLAS---------QMSQPGGMIAFELKGGIGAGRRFMNALQLFSRAVSLGDAESLAQHPASMTHSSYTPEERAHYGISEGLVRLSVGLEDIDDLLADVQQALKASA 398
                                    16        26        36     |   -         -      | 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       326       336       346       356       366       376       386       396  
                                                              42                   63                                                                                                                                                 211-LLP                                                                              296       306                                                                                            


Chain D from PDB  Type:PROTEIN  Length:356
 aligned with MEGL_PSEPU | P13254 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:392
                                    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       326       336       346       356       366       376       386       396  
           MEGL_PSEPU     7 LPGFATRAIHHGYDPQDHGGALVPPVYQTATFTFPTVEYGAACFAGEQAGHFYSRISNPTLNLLEARMASLEGGEAGLALASGMGAITSTLWTLLRPGDEVLLGNTLYGCTFAFLHHGIGEFGVKLRHVDMADLQALEAAMTPATRVIYFESPANPNMHMADIAGVAKIARKHGATVVVDNTYCTPYLQRPLELGADLVVHSATKYLSGHGDITAGIVVGSQALVDRIRLQGLKDMTGAVLSPHDAALLMRGIKTLNLRMDRHCANAQVLAEFLARQPQVELIHYPGLASFPQYTLARQQMSQPGGMIAFELKGGIGAGRRFMNALQLFSRAVSLGDAESLAQHPASMTHSSYTPEERAHYGISEGLVRLSVGLEDIDDLLADVQQALKASA 398
               SCOP domains d1gc0d_ D: Methionine gamma-lyase,                      MGL                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -1gc0D01 D:8-262 Type I PLP-depende                     nt aspartate aminotransferase-like (Major domain)                                                                                                                                                       1gc0D02 D:263-395 Aspartate Ami               notransferase, domain 1                                                                --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh..hhhhhh................---------------------.hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhh.eeee....hhhhhhhhh...eeeeeee..........hhhhhhhhhh....eeeee...hhhhhhhhhhhh..eeeee.............eeeeehhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee..---------------....eeeeee.hhhhhhhhhhhhh...ee.........eeehhhhh.....hhhhhhhh.....eeeee....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYS_MET_METAB_P------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gc0 D   7 LPGFATRAIHHGYDPQDHGGALVPPVYQTATFTFP---------------------SNPTLNLLEARMASLEGGEAGLALASGMGAITSTLWTLLRPGDEVLLGNTLYGCTFAFLHHGIGEFGVKLRHVDMADLQALEAAMTPATRVIYFESPANPNMHMADIAGVAKIARKHGATVVVDNTYCTPYLQRPLELGADLVVHSATkYLSGHGDITAGIVVGSQALVDRIRLQGLKDMTGAVLSPHDAALLMRGIKTLNLRMDRHCANAQVLAEFLARQPQVELIHYPG---------------QPGGMIAFELKGGIGAGRRFMNALQLFSRAVSLGDAESLAQHPASMTHSSYTPEERAHYGISEGLVRLSVGLEDIDDLLADVQQALKASA 398
                                    16        26        36    |    -         -      | 66        76        86        96       106       116       126       136       146       156       166       176       186       196       206    |  216       226       236       246       256       266       276       286      |  -         -  |    316       326       336       346       356       366       376       386       396  
                                                             41                    63                                                                                                                                                 211-LLP                                                                           293             309
   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, 4)

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

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GC0)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (MEGL_PSEPU | P13254)
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:0047982    homocysteine desulfhydrase activity    Catalysis of the reaction: L-homocysteine + H2O = sulfide + NH3 + 2-oxobutanoate.
    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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  4.4.1.11
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 Related Entries

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

UniProtKB/Swiss-Prot
        MEGL_PSEPU | P13254: 1gc2 1pg8 1ukj 2o7c 3vk2 3vk3 3vk4 5x2v 5x2w 5x2x 5x2y 5x2z 5x30

(-) Related Entries Specified in the PDB File

1gc2 L-METHIONINE GAMMA-LYASE (SPACE GROUP P 43 21 2)