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Title :   CYSTATHIONINE BETA-LYASE (CBL) FROM ESCHERICHIA COLI

Authors :   T. Clausen, R. Huber, A. Messerschmidt

Date :   02 Sep 97 (Deposition) - 09 Sep 98 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.83

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (2x)

Keywords :   Plp-Dependent Enzymes, Methionine Biosynthesis, C-S Beta Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Clausen, R. Huber, B. Laber, H. D. Pohlenz, A. Messerschmidt
Crystal Structure Of The Pyridoxal-5'-Phosphate Dependent Cystathionine Beta-Lyase From Escherichia Coli At 1. 83 A.
J. Mol. Biol. V. 262 202 1996
PubMed-ID: 8831789 | Reference-DOI: 10.1006/JMBI.1996.0508
(for further references see the PDB file header)

Molecule 1 - CYSTATHIONINE BETA-LYASE
	Chains	:	A, B
	EC Number	:	4.4.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	DH5
	Expression System Taxid	:	562
	Expression System Vector	:	PDR540
	Gene	:	METC
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Other Details	:	PLP BOUND AS COFACTOR TO LYS 210
	Strain	:	K12
	Synonym	:	BETA CYSTATHIONASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	BCT	2	Ligand/Ion	BICARBONATE ION
2	LLP	2	Mod. Amino Acid	2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	BCT	4	Ligand/Ion	BICARBONATE ION
2	LLP	4	Mod. Amino Acid	2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:111 , LLP A:210 , SER A:339 , TRP A:340 , ARG A:372	BINDING SITE FOR RESIDUE BCT A 402
2	AC2	SOFTWARE	TYR B:111 , LLP B:210 , SER B:339 , TRP B:340 , ARG B:372	BINDING SITE FOR RESIDUE BCT B 403
3	PLA	UNKNOWN	LLP A:210	BINDING SITE
4	PLB	UNKNOWN	LLP B:210	BINDING SITE

(no "SS Bond" information available for 1CL1)

Asymmetric Unit

No.	Residues
1	Ser A:155	-	Pro A:156
2	Ser B:155	-	Pro B:156

(no "SAP(SNP)/Variant" information available for 1CL1)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYS_MET_METAB_PP	PS00868	Cys/Met metabolism enzymes pyridoxal-phosphate attachment site.	METC_ECOLI	202-216	2	A:202-216 B:202-216

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYS_MET_METAB_PP	PS00868	Cys/Met metabolism enzymes pyridoxal-phosphate attachment site.	METC_ECOLI	202-216	4	A:202-216 B:202-216

(no "Exon" information available for 1CL1)

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:391
 aligned with METC_ECOLI | P06721 from UniProtKB/Swiss-Prot  Length:395

    Alignment length:391
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394 
           METC_ECOLI     5 KLDTQLVNAGRSKKYTLGAVNSVIQRASSLVFDSVEAKKHATRNRANGELFYGRRGTLTHFSLQQAMCELEGGAGCVLFPCGAAAVANSILAFIEQGDHVLMTNTAYEPSQDFCSKILSKLGVTTSWFDPLIGADIVKHLQPNTKIVFLESPGSITMEVHDVPAIVAAVRSVVPDAIIMIDNTWAAGVLFKALDFGIDVSIQAATKYLVGHSDAMIGTAVCNARCWEQLRENAYLMGQMVDADTAYITSRGLRTLGVRLRQHHESSLKVAEWLAEHPQVARVNHPALPGSKGHEFWKRDFTGSSGLFSFVLKKKLNNEELANYLDNFSLFSMAYSWGGYESLILANQPEHIAAIRPQGEIDFSGTLIRLHIGLEDVDDLIADLDAGFARIV 395
               SCOP domains d1cl1a_ A: Cystathionine beta-lyase, CBL                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1cl1A01 A:5-258 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                           1cl1A02 A:259-395 Aspartate Aminotransferase, domain 1                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh....hhhh..................hhhhhhhhh..............hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh.....eeeee....hhhhhhhhh.hhhh..eeeee....hhhhhh.....eeeeeee...........hhhhhhhhhhh....eeeee..........hhhh...eeeee.............eeeee....hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.........hhhhhhh......eeeeee.....hhhhhhhhhh...............eeeee.hhhhhhh...........eeeee.....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYS_MET_METAB_P----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cl1 A   5 KLDTQLVNAGRSKKYTLGAVNSVIQRASSLVFDSVEAKKHATRNRANGELFYGRRGTLTHFSLQQAMCELEGGAGCVLFPCGAAAVANSILAFIEQGDHVLMTNTAYEPSQDFCSKILSKLGVTTSWFDPLIGADIVKHLQPNTKIVFLESPGSITMEVHDVPAIVAAVRSVVPDAIIMIDNTWAAGVLFKALDFGIDVSIQAATkYLVGHSDAMIGTAVCNARCWEQLRENAYLMGQMVDADTAYITSRGLRTLGVRLRQHHESSLKVAEWLAEHPQVARVNHPALPGSKGHEFWKRDFTGSSGLFSFVLKKKLNNEELANYLDNFSLFSMAYSWGGYESLILANQPEHIAAIRPQGEIDFSGTLIRLHIGLEDVDDLIADLDAGFARIV 395
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204     | 214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394 
                                                                                                                                                                                                                                       210-LLP

Chain B from PDB  Type:PROTEIN  Length:392
 aligned with METC_ECOLI | P06721 from UniProtKB/Swiss-Prot  Length:395

    Alignment length:392
                                    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  
           METC_ECOLI     4 KKLDTQLVNAGRSKKYTLGAVNSVIQRASSLVFDSVEAKKHATRNRANGELFYGRRGTLTHFSLQQAMCELEGGAGCVLFPCGAAAVANSILAFIEQGDHVLMTNTAYEPSQDFCSKILSKLGVTTSWFDPLIGADIVKHLQPNTKIVFLESPGSITMEVHDVPAIVAAVRSVVPDAIIMIDNTWAAGVLFKALDFGIDVSIQAATKYLVGHSDAMIGTAVCNARCWEQLRENAYLMGQMVDADTAYITSRGLRTLGVRLRQHHESSLKVAEWLAEHPQVARVNHPALPGSKGHEFWKRDFTGSSGLFSFVLKKKLNNEELANYLDNFSLFSMAYSWGGYESLILANQPEHIAAIRPQGEIDFSGTLIRLHIGLEDVDDLIADLDAGFARIV 395
               SCOP domains d1cl1b_ B: Cystathionine beta-lyase, CBL                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1cl1B01 B:4-258 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                            1cl1B02 B:259-395 Aspartate Aminotransferase, domain 1                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh....hhhh..................hhhhhhhhh..............hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh.....eeeee....hhhhhhhhh.hhhh..eeeee....hhhhhhh....eeeeeee...........hhhhhhhhhhh....eeeee..........hhhh...eeeee.............eeeee....hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.........hhhhhhh......eeeeee.....hhhhhhhhhh...............eeeee.hhhhhhh...........eeeee.....hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYS_MET_METAB_P----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cl1 B   4 KKLDTQLVNAGRSKKYTLGAVNSVIQRASSLVFDSVEAKKHATRNRANGELFYGRRGTLTHFSLQQAMCELEGGAGCVLFPCGAAAVANSILAFIEQGDHVLMTNTAYEPSQDFCSKILSKLGVTTSWFDPLIGADIVKHLQPNTKIVFLESPGSITMEVHDVPAIVAAVRSVVPDAIIMIDNTWAAGVLFKALDFGIDVSIQAATkYLVGHSDAMIGTAVCNARCWEQLRENAYLMGQMVDADTAYITSRGLRTLGVRLRQHHESSLKVAEWLAEHPQVARVNHPALPGSKGHEFWKRDFTGSSGLFSFVLKKKLNNEELANYLDNFSLFSMAYSWGGYESLILANQPEHIAAIRPQGEIDFSGTLIRLHIGLEDVDDLIADLDAGFARIV 395
                                    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  
                                                                                                                                                                                                                                        210-LLP

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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(

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Folds(

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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: Cystathionine beta-lyase, CBL (5)

Escherichia coli [TaxId: 562] (4)

1a	d1cl1a_	A:
1b	d1cl1b_	B:

(no "Pfam Domain" information available for 1CL1)

Asymmetric Unit(hide GO term definitions)

Chain A,B (METC_ECOLI | P06721)

molecular function
	GO:0080146	L-cysteine desulfhydrase activity	Catalysis of the reaction: L-cysteine + H2O = ammonia + pyruvate + hydrogen sulfide + H+.
	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:0004121	cystathionine beta-lyase activity	Catalysis of the reaction: cystathionine + H2O = L-homocysteine + NH3 + pyruvate.
	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: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.
biological process
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0006520	cellular amino acid metabolic process	The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
	GO:0009086	methionine biosynthetic process	The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	1cl1
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	METC_ECOLI \| P06721	:	1cl2 2fq6 2gqn 4itg 4itx

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Description

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Ligands, Modified Residues, Ions (2, 4)

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