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Title :   CRYSTAL STRUCTURE OF L-METHIONINE GAMMA-LYASE FROM CITROBACTER FREUNDII WITH GLYCINE

Authors :   S. V. Revtovich, E. A. Morozova, N. V. Anufrieva, A. D. Nikulin, T. V. Dem

Date :   05 Oct 12 (Deposition) - 06 Nov 13 (Release) - 12 Nov 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Complex, Pyridoxal-5'-Phosphate, Plp-Dependent Enzyme, Lyase, L- Methionine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. V. Revtovich, N. G. Faleev, E. A. Morozova, N. V. Anufrieva, A. D. Nikulin, T. V. Demidkina
Crystal Structure Of The External Aldimine Of Citrobacter Freundii Methionine Gamma-Lyase With Glycine Provides Insight In Mechanisms Of Two Stages Of Physiological Reaction And Isotope Exchange Of Alpha- And Beta-Protons Of Competitive Inhibitors.
Biochimie V. 101 161 2014
PubMed-ID: 24463191 | Reference-DOI: 10.1016/J.BIOCHI.2014.01.007

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	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MEGL
	Organism Scientific	:	CITROBACTER FREUNDII
	Organism Taxid	:	546

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 6)

No.	Name	Count	Type	Full Name
1	CSO	1	Mod. Amino Acid	S-HYDROXYCYSTEINE
2	GLY	1	Mod. Amino Acid	GLYCINE
3	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PLG	1	Ligand/Ion	N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]

Biological Unit 1 (4, 24)

No.	Name	Count	Type	Full Name
1	CSO	4	Mod. Amino Acid	S-HYDROXYCYSTEINE
2	GLY	4	Mod. Amino Acid	GLYCINE
3	PEG	12	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PLG	4	Ligand/Ion	N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:58 , ARG A:60 , SER A:87 , GLY A:88 , ILE A:89 , TYR A:113 , GLU A:156 , ASN A:160 , ASP A:185 , PHE A:188 , SER A:207 , THR A:209 , LYS A:210 , SER A:339 , LEU A:340 , ARG A:374 , HOH A:616	BINDING SITE FOR RESIDUE PLG A 401
2	AC2	SOFTWARE	HIS A:355 , VAL A:358 , HOH A:651	BINDING SITE FOR RESIDUE GLY A 402
3	AC3	SOFTWARE	PRO A:191 , TYR A:192 , CYS A:193 , SER A:307 , HOH A:635	BINDING SITE FOR RESIDUE PEG A 403
4	AC4	SOFTWARE	GLN A:18 , SER A:28 , HIS A:215 , ASP A:217 , TRP A:252 , LEU A:255 , ARG A:256 , LYS A:259 , HOH A:537 , HOH A:550	BINDING SITE FOR RESIDUE PEG A 404
5	AC5	SOFTWARE	ASN A:10 , ARG A:267 , ASN A:271 , LEU A:379 , GLU A:380 , ASP A:381 , PRO A:382 , GLU A:383 , HOH A:569	BINDING SITE FOR RESIDUE PEG A 405

(no "SS Bond" information available for 4HF8)

Asymmetric Unit

No.	Residues
1	Ser A:54	-	Gly A:55
2	Thr A:157	-	Pro A:158

(no "SAP(SNP)/Variant" information available for 4HF8)

(no "PROSITE Motif" information available for 4HF8)

(no "Exon" information available for 4HF8)

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
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Chain A from PDB  Type:PROTEIN  Length:397
                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4hf8a_ A: Methionine gamma-lyase, MGL                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhh........................hhhhhhhhhh............hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhh.eeeee...hhhhhhhhh...eeeeeee..........hhhhhhhhhhhh..eeeee.........hhhhhh..eeeee.............eeeeehhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhh.....eeeeee.hhhhhhhhhhhhh...ee.........eee..........hhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hf8 A   2 SDcRTYGFNTQIVHAGQQPDPSTGALSTPIFQTSTFVFDSAEQGAARFALEESGYIYTRLGNPTTDALEKKLAVLERGEAGLATASGISAITTTLLTLCQQGDHIVSASAIYGCTHAFLSHSMPKFGINVRFVDAAKPEEIRAAMRPETKVVYIETPANPTLSLVDIETVAGIAHQQGALLVVDNTFMSPYCQQPLQLGADIVVHSVTKYINGHGDVIGGIIVGKQEFIDQARFVGLKDITGGCMSPFNAWLTLRGVKTLGIRMERHCENALKIARFLEGHPSITRVYYPGLSSHPQYELGQRQMSLPGGIISFEIAGGLEAGRRMINSVELCLLAVSLGDTETLIQHPASMTHSPVAPEERLKAGITDGLIRLSVGLEDPEDIINDLEHAIRKATG 402
                              |     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     ||
                              |                                                                                                                                                                                                                                                                                                                                                                                                      397|
                              4-CSO                                                                                                                                                                                                                                                                                                                                                                                                   402

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: PLP-dependent transferase-like (627)

Superfamily: PLP-dependent transferases (625)

Family: Cystathionine synthase-like (64)

Protein domain: Methionine gamma-lyase, MGL (14)

Citrobacter freundii [TaxId: 546] (7)

d4hf8a_

(no "CATH Domain" information available for 4HF8)

(no "Pfam Domain" information available for 4HF8)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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		GLY	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		PLG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ser A:54 - Gly A:55	[ RasMol ]
		Thr A:157 - Pro A:158	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	4hf8
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	4.4.1.11
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		Interatomic Contacts of Structural Units	:	CSU
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	Q84AR1_CITFR \| Q84AR1	:	1y4i 2rfv 3jw9 3jwa 3jwb 3mkj 4mkj 4mkk 4oma

1y4i	STRUCTURE OF L-METHIONINE GAMMA-LYASE FROM CITROBACTER FREUNDII
2rfv	HIGH RESOLUTION STRUCTURE OF L-METHIONINE GAMMA-LYASE FROM CITROBACTER FREUNDII
3jw9	CRYSTAL STRUCTURE OF L-METHIONINE GAMMA-LYASE FROM CITROBACTER FREUNDII WITH S-ETHYL-CYSTEINE
3jwa	CRYSTAL STRUCTURE OF L-METHIONINE GAMMA-LYASE FROM CITROBACTER FREUNDII WITH METHIONINE PHOSPHINATE
3jwb	CRYSTAL STRUCTURE OF L-METHIONINE GAMMA-LYASE FROM CITROBACTER FREUNDII WITH NORLEUCINE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 1)

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Pfam Domains (0, 0)

Gene Ontology (4, 4)

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