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(-) Description

Title :  CRYSTAL STRUCTURE OF L-METHIONINE GAMMA-LYASE FROM CITROBACTER FREUNDII WITH S-ETHYL-CYSTEINE
 
Authors :  S. V. Revtovish, A. D. Nikulin, E. A. Morozova, T. V. Demidkina
Date :  18 Sep 09  (Deposition) - 08 Sep 10  (Release) - 05 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Pyridoxal-5'-Phosphate, Plp-Dependent Enzyme, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. V. Revtovich, E. A. Morozova, E. N. Khurs, L. N. Zakomirdina, A. D. Nikulin, T. V. Demidkina, R. M. Khomutov
Three-Dimensional Structures Of Noncovalent Complexes Of Citrobacter Freundii Methionine Gamma-Lyase With Substrates
Biochemistry Mosc. V. 76 564 2011
PubMed-ID: 21639836  |  Reference-DOI: 10.1134/S0006297911050063

(-) Compounds

Molecule 1 - METHIONINE GAMMA-LYASE
    Chains: A
    EC Number: 4.4.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-MGL
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MEGL
    Organism Scientific: CITROBACTER FREUNDII
    Organism Taxid: 546

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1ECX1Ligand/IonS-ETHYL-L-CYSTEINE
2LLP1Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1ECX4Ligand/IonS-ETHYL-L-CYSTEINE
2LLP4Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3PEG4Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:58 , TYR A:113 , LLP A:210 , VAL A:338 , SER A:339 , LEU A:340 , ARG A:374 , HOH A:725BINDING SITE FOR RESIDUE ECX A 399
2AC2SOFTWAREPRO A:191 , TYR A:192 , ARG A:304 , GLN A:305 , HOH A:677BINDING SITE FOR RESIDUE PEG A 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JW9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:157 -Pro A:158
2Asn A:160 -Pro A:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JW9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JW9)

(-) Exons   (0, 0)

(no "Exon" information available for 3JW9)

(-) 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:396
 aligned with Q84AR1_CITFR | Q84AR1 from UniProtKB/TrEMBL  Length:398

    Alignment length:396
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391      
         Q84AR1_CITFR     2 SDCRTYGFNTQIVHAGQQPDPSTGALSTPIFQTSTFVFDSAEQGAARFALEESGYIYTRLGNPTTDALEKKLAVLERGEAGLATASGISAITTTLLTLCQQGDHIVSASAIYGCTHAFLSHSMPKFGINVRLVDAGKPEEIRAAMRPETKVVYIETPANPTLSLVDIETVAGIAHQQGALLVVDNTFMSPYCQQPLQLGADIVVHSVTKYINGHGDVIGGIIVGKQEFIDQARFVGLKDITGGCMSPFNAWLTLRGVKTLGIRMERHCENALKIARFLEGHPSITRVYYPGLSSHPQYELGQRQMSLPGGIISFEIAGGLEAGRRMINSVELCLLAVSLGDTETLIQHPASMTHSPVAPEERLKAGITDGLIRLSVGLEDPEDIINDLEHAIRKAT 397
               SCOP domains d3jw9a_ A: Methionine gamma-lyase, MGL                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --------Cys_Met_Meta_PP-3jw9A01 A:10-394                                                                                                                                                                                                                                                                                                                                                                 --- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh........................hhhhhhhhhh............hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh..eeeee...hhhhhhhhh...eeeeeee..........hhhhhhhhhhhh..eeeee.........hhhhhh..eeeee.............eeeeehhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhh.....eeeeee.hhhhhhhhhhh.....ee.........eeehhhhhh....hhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3jw9 A   2 SDCRTYGFNTQIVHAGQQPDPSTGALSTPIFQTSTFVFDSAEQGAARFALEESGYIYTRLGNPTTDALEKKLAVLERGEAGLATASGISAITTTLLTLCQQGDHIVSASAIYGCTHAFLSHSMPKFGINVSFVDAAKPEEIRAAMRPETKVVYIETPANPTLSLVDIETVAGIAHQQGALLVVDNTFMSPYCQQPLQLGADIVVHSVTkYINGHGDVIGGIIVGKQEFIDQARFVGLKDITGGCMSPFNAWLTLRGVKTLGIRMERHCENALKIARFLEGHPSITRVYYPGLSSHPQYELGQRQMSLPGGIISFEIAGGLEAGRRMINSVELCLLAVSLGDTETLIQHPASMTHSPVAPEERLKAGITDGLIRLSVGLEDPEDIINDLEHAIRKAT 397
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391      
                                                                                                                                                                                                                                          210-LLP
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3JW9)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: PLP_aminotran (240)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q84AR1_CITFR | Q84AR1)
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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 Related Entries

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

UniProtKB/TrEMBL
        Q84AR1_CITFR | Q84AR1: 1y4i 2rfv 3jwa 3jwb 3mkj 4hf8 4mkj 4mkk 4oma

(-) Related Entries Specified in the PDB File

1e5e METHIONINE GAMMA-LYASE (MGL) FROM TRICHOMONAS VAGINALIS IN COMPLEX WITH PROPARGYLGLYCINE
1ukj DETAILED STRUCTURE OF L-METHIONINE -LYASE FROM PSEUDOMONAS PUTIDA
1y4i STRUCTURE OF L-METHIONINE GAMMA-LYASE FROM CITROBACTER FREUNDII
2o7c CRYSTAL STRUCTURE OF L-METHIONINE-LYASE FROM PSEUDOMONAS PUTIDA
2rfv HIGH RESOLUTION STRUCTURE OF L-METHIONINE GAMMA-LYASE FROM CITROBACTER FREUNDII
3jwa
3jwb