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(-) Description

Title :  CRYSTAL STRUCTURE OF C115A MUTANT L-METHIONINE GAMMA-LYASE FROM CITROBACTER FREUNDII MODIFIED BY ALLICINE
 
Authors :  S. V. Revtovich, A. D. Nikulin, E. A. Morozova, L. N. Zakomirdina, T. V. D
Date :  05 Sep 13  (Deposition) - 12 Nov 14  (Release) - 31 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Pyridoxal-5'-Phosphate, Plp-Dependent Enzyme, Aminotransferase Class- V, Lyase, Allicine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. A. Morozova, S. V. Revtovich, N. V. Anufrieva, V. V. Kulikova, A. D. Nikulin, T. V. Demidkina
Alliin Is A Suicide Substrate Of Citrobacter Freundii Methionine Gamma-Lyase: Structural Bases Of Inactivation Of The Enzyme.
Acta Crystallogr. , Sect. D V. 70 3034 2014
PubMed-ID: 25372692  |  Reference-DOI: 10.1107/S1399004714020938

(-) Compounds

Molecule 1 - METHIONINE GAMMA-LYASE
    ChainsA
    EC Number4.4.1.11
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-C115AMGL
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneMEGL
    MutationYES
    Organism ScientificCITROBACTER FREUNDII
    Organism Taxid546

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 12)

Asymmetric Unit (6, 12)
No.NameCountTypeFull Name
1C1S2Mod. Amino Acid3-(PROP-2-EN-1-YLDISULFANYL)-L-ALANINE
2CL1Ligand/IonCHLORIDE ION
3K1Ligand/IonPOTASSIUM ION
4LLP1Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
5NA5Ligand/IonSODIUM ION
6PGE2Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (3, 20)
No.NameCountTypeFull Name
1C1S8Mod. Amino Acid3-(PROP-2-EN-1-YLDISULFANYL)-L-ALANINE
2CL-1Ligand/IonCHLORIDE ION
3K-1Ligand/IonPOTASSIUM ION
4LLP4Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
5NA-1Ligand/IonSODIUM ION
6PGE8Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:191 , TYR A:192 , CYS A:193 , GLN A:195 , GLN A:303 , SER A:307 , HOH A:751 , HOH A:827BINDING SITE FOR RESIDUE PGE A 401
2AC2SOFTWAREGLU A:270 , LYS A:274 , PRO A:382 , GLU A:383BINDING SITE FOR RESIDUE PGE A 402
3AC3SOFTWARESER A:35 , THR A:36 , THR A:209 , SER A:339 , ASP A:342BINDING SITE FOR RESIDUE NA A 403
4AC4SOFTWAREALA A:84 , C1S A:245 , MET A:246BINDING SITE FOR RESIDUE NA A 404
5AC5SOFTWAREILE A:317 , GLY A:319 , GLY A:320 , HOH A:582 , HOH A:627BINDING SITE FOR RESIDUE NA A 405
6AC6SOFTWAREARG A:267 , LEU A:379 , GLU A:380 , NA A:407BINDING SITE FOR RESIDUE CL A 406
7AC7SOFTWAREPRO A:382 , CL A:406 , HOH A:537 , HOH A:598 , HOH A:672BINDING SITE FOR RESIDUE NA A 407
8AC8SOFTWAREPRO A:64 , ASP A:67 , HOH A:759BINDING SITE FOR RESIDUE NA A 408
9AC9SOFTWARETYR A:113 , VAL A:338BINDING SITE FOR RESIDUE K A 409

(-) SS Bonds  (0, 0)

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

(-) 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 4MKK)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MKK)

(-) 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:388
                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh........................hhhhhhhhh.....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
                 4mkk A   2 SDcRTYGFNTQIVHAGQQPDPSTGALSTPIFQTSTFVFDSAEQGAARFYTRLGNPTTDALEKKLAVLERGEAGLATASGISAITTTLLTLCQQGDHIVSASAIYGATHAFLSHSMPKFGINVSFVDAAKPEEIRAAMRPETKVVYIETPANPTLSLVDIETVAGIAHQQGALLVVDNTFMSPYCQQPLQLGADIVVHSVTkYINGHGDVIGGIIVGKQEFIDQARFVGLKDITGGcMSPFNAWLTLRGVKTLGIRMERHCENALKIARFLEGHPSITRVYYPGLSSHPQYELGQRQMSLPGGIISFEIAGGLEAGRRMINSVELCLLAVSLGDTETLIQHPASMTHSPVAPEERLKAGITDGLIRLSVGLEDPEDIINDLEHAIRKAT 397
                              |     11        21        31        41       |59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209|      219       229       239     | 249       259       269       279       289       299       309       319       329       339       349       359       369       379       389        
                              |                                           49|                                                                                                                                                     210-LLP                            245-C1S                                                                                                                                                    
                              4-C1S                                        58                                                                                                                                                                                                                                                                                                                                                   

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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  (0, 0)

(no "SCOP Domain" information available for 4MKK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

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 Related Entries

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

UniProtKB/TrEMBL
        Q84AR1_CITFR | Q84AR11y4i 2rfv 3jw9 3jwa 3jwb 3mkj 4hf8 4mkj 4oma

(-) Related Entries Specified in the PDB File

2rfv HIGH RESOLUTION STRUCTURE OF L-METHIONINE GAMMA-LYASE FROM CITROBACTER FREUNDII (WILD-TYPE)
4mkj