2GQN - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Title :   CYSTATHIONINE BETA-LYASE (CBL) FROM ESCHERICHIA COLI IN COMPLEX WITH N-HYDRAZINOCARBONYLMETHYL-2-NITRO-BENZAMIDE

Authors :   R. Summerfield, M. S. Junop

Date :   21 Apr 06 (Deposition) - 06 Mar 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Protein-Inhibitor Complex, Plp Cofactor Covalently Bount To Blp Inhibitor, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. J. Ejim, J. E. Blanchard, K. P. Koteva, R. Sumerfield, N. H. Elowe, J. D. Chechetto, E. D. Brown, M. S. Junop, G. D. Wright
Inhibitors Of Bacterial Cystathionine Beta-Lyase: Leads For New Antimicrobial Agents And Probes Of Enzyme Structure And Function.
J. Med. Chem. V. 50 755 2007
PubMed-ID: 17300162 | Reference-DOI: 10.1021/JM061132R

Molecule 1 - CYSTATHIONINE BETA-LYASE
	Chains	:	A, B
	EC Number	:	4.4.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	METC
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	CBL, BETA-CYSTATHIONASE, CYSTEINE LYASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	BLP	2	Ligand/Ion	(5-HYDROXY-6-METHYL-4-((2-(2-(2-NITROBENZAMIDO)ACETYL)HYDRAZINYL)METHYL)PYRIDIN-3-YL)METHYL DIHYDROGENPHOSPHATE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	BLP	4	Ligand/Ion	(5-HYDROXY-6-METHYL-4-((2-(2-(2-NITROBENZAMIDO)ACETYL)HYDRAZINYL)METHYL)PYRIDIN-3-YL)METHYL DIHYDROGENPHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:55 , TYR A:56 , ARG A:58 , CYS A:85 , GLY A:86 , ALA A:87 , TYR A:111 , GLU A:112 , GLU A:154 , ASP A:185 , ALA A:207 , THR A:209 , LYS A:210 , MET A:219 , TYR A:338 , SER A:339 , TRP A:340 , ARG A:372 , HOH A:873 , HOH A:1134 , HOH A:1153	BINDING SITE FOR RESIDUE BLP A 700
2	AC2	SOFTWARE	TYR B:56 , ARG B:58 , CYS B:85 , GLY B:86 , ALA B:87 , TYR B:111 , PRO B:113 , GLU B:154 , ASP B:185 , ALA B:207 , THR B:209 , LYS B:210 , MET B:219 , TYR B:238 , TYR B:338 , SER B:339 , TRP B:340 , ARG B:372 , HOH B:725 , HOH B:742 , HOH B:870	BINDING SITE FOR RESIDUE BLP B 700

(no "SS Bond" information available for 2GQN)

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 2GQN)

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 2GQN)

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 d2gqna_ A: Cystathionine beta-lyase, CBL                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2gqnA01 A:5-258 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                           2gqnA02 A:259-395 Aspartate Aminotransferase, domain 1                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh..hhhhhh................hhhhhhhhhhh............hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhh.eeeee...hhhhhhhhh...eeeeeee..........hhhhhhhhhhhhh...eeeee.........hhhhhh..eeeee.............eeeeehhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhh.....eeeeee....hhhhhhhhhh.....ee.........eeeeehhhhhhh............eeeee....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYS_MET_METAB_P----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gqn 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

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 d2gqnb_ B: Cystathionine beta-lyase, CBL                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 2gqnB01 B:4-258 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                            2gqnB02 B:259-395 Aspartate Aminotransferase, domain 1                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh..hhhhhh................hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhh.eeeee...hhhhhhhhh...eeeeeee..........hhhhhhhhhhhhh...eeeee.........hhhhhh..eeeee.............eeeeehhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee........hhhhhhhhh.....eeeeee....hhhhhhhhhh.....ee.........eeeeehhhhhhh............eeeee....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYS_MET_METAB_P----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gqn 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

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: Cystathionine beta-lyase, CBL (5)

Escherichia coli [TaxId: 562] (4)

1a	d2gqna_	A:
1b	d2gqnb_	B:

(no "Pfam Domain" information available for 2GQN)

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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Access by PDB/NDB ID
	2gqn
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	4.4.1.8
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UniProtKB/Swiss-Prot
	METC_ECOLI \| P06721	:	1cl1 1cl2 2fq6 4itg 4itx

2fq6	SAME PROTEIN COMPLEXED WITH N-HYDRAZINOCARBONYLMETHYL-2- TRIFLUOROMETHYL-BENZAMIDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (9, 9)

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