2VLF - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   QUINONOID INTERMEDIATE OF CITROBACTER FREUNDII TYROSINE PHENOL-LYASE FORMED WITH ALANINE

Authors :   D. Milic, T. V. Demidkina, D. Matkovic-Calogovic, A. A. Antson

Date :   14 Jan 08 (Deposition) - 19 Aug 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.89

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

Keywords :   Plp-Dependent Enzyme, Lyase, Tyrosine Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Milic, T. V. Demidkina, N. G. Faleev, D. Matkovic-Calogovic, A. A. Antson
Insights Into The Catalytic Mechanism Of Tyrosine Phenol-Lyase From X-Ray Structures Of Quinonoid Intermediates.
J. Biol. Chem. V. 283 29206 2008
PubMed-ID: 18715865 | Reference-DOI: 10.1074/JBC.M802061200

Molecule 1 - TYROSINE PHENOL-LYASE
	Chains	:	A, B
	EC Number	:	4.1.99.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTZTPL
	Expression System Strain	:	SVS 370
	Expression System Taxid	:	562
	Organism Scientific	:	CITROBACTER FREUNDII
	Organism Taxid	:	546
	Synonym	:	BETA-TYROSINASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 6)

No.	Name	Count	Type	Full Name
1	K	2	Ligand/Ion	POTASSIUM ION
2	P33	1	Ligand/Ion	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
3	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL
4	PLI	2	Ligand/Ion	(2E)-2-{[(Z)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4(1H)-YLIDENE}METHYL]IMINO}PROPANOIC ACID

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION
2	P33	2	Ligand/Ion	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
3	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL
4	PLI	4	Ligand/Ion	(2E)-2-{[(Z)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4(1H)-YLIDENE}METHYL]IMINO}PROPANOIC ACID

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:52 , ASN A:262 , HOH A:2080 , GLU B:69 , HOH B:2367	BINDING SITE FOR RESIDUE K B1457
2	AC2	SOFTWARE	THR A:49 , GLN A:98 , GLY A:99 , ARG A:100 , GLU A:103 , PHE A:123 , THR A:125 , ASN A:185 , ASP A:214 , THR A:216 , ARG A:217 , SER A:254 , LYS A:257 , ARG A:404 , HOH A:2448 , TYR B:71	BINDING SITE FOR RESIDUE PLI A1457
3	AC3	SOFTWARE	GLU A:69 , HOH A:2302 , GLY B:52 , ASN B:262 , HOH B:2100 , HOH B:2341	BINDING SITE FOR RESIDUE K B1458
4	AC4	SOFTWARE	TYR A:71 , THR B:49 , GLN B:98 , GLY B:99 , ARG B:100 , GLU B:103 , PHE B:123 , THR B:125 , ASN B:185 , ASP B:214 , THR B:216 , ARG B:217 , SER B:254 , LYS B:257 , ARG B:404 , HOH B:2514	BINDING SITE FOR RESIDUE PLI B1459
5	AC5	SOFTWARE	MET A:1 , TYR A:3 , TYR A:324 , TYR A:414 , ASP A:418 , TYR B:3 , TYR B:414 , HOH B:2515	BINDING SITE FOR RESIDUE P33 B1460
6	AC6	SOFTWARE	VAL A:16 , SER A:17 , TYR A:44 , HOH A:2033 , HOH A:2451 , GLN B:311 , GLU B:313	BINDING SITE FOR RESIDUE PGE A1458

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

Asymmetric Unit

No.	Residues
1	Val A:182	-	Thr A:183
2	Glu A:338	-	Pro A:339
3	Val B:182	-	Thr B:183
4	Glu B:338	-	Pro B:339

(no "SAP(SNP)/Variant" information available for 2VLF)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_ELIM_LYASE	PS00853	Beta-eliminating lyases pyridoxal-phosphate attachment site.	TPL_CITFR	247-265	2	A:247-265 B:247-265

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_ELIM_LYASE	PS00853	Beta-eliminating lyases pyridoxal-phosphate attachment site.	TPL_CITFR	247-265	4	A:247-265 B:247-265

(no "Exon" information available for 2VLF)

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:456
 aligned with TPL_CITFR | P31013 from UniProtKB/Swiss-Prot  Length:456

    Alignment length:456
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450      
            TPL_CITFR     1 MNYPAEPFRIKSVETVSMIPRDERLKKMQEAGYNTFLLNSKDIYIDLLTDSGTNAMSDKQWAGMMMGDEAYAGSENFYHLERTVQELFGFKHIVPTHQGRGAENLLSQLAIKPGQYVAGNMYFTTTRYHQEKNGAVFVDIVRDEAHDAGLNIAFKGDIDLKKLQKLIDEKGAENIAYICLAVTVNLAGGQPVSMANMRAVRELTEAHGIKVFYDATRCVENAYFIKEQEQGFENKSIAEIVHEMFSYADGCTMSGKKDCLVNIGGFLCMNDDEMFSSAKELVVVYEGMPSYGGLAGRDMEAMAIGLREAMQYEYIEHRVKQVRYLGDKLKAAGVPIVEPVGGHAVFLDARRFCEHLTQDEFPAQSLAASIYVETGVRSMERGIISAGRNNVTGEHHRPKLETVRLTIPRRVYTYAHMDVVADGIIKLYQHKEDIRGLKFIYEPKQLRFFTARFDYI 456
               SCOP domains d2vlfa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2vlfA01 A:1-57,A:311-455                                 2vlfA02 A:58-310 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                         2vlfA01 A:1-57,A:311-455 Aspartate Aminotransferase, domain 1                                                                                    - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhh..hhhhhhhhhh.ee..........hhhhhhhhh........hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeee...hhhhhhhhhhh..eeee..hhhhhh...........hhhhhhhhhhhhh...eeeeeee...........hhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhh......hhhhhhhhhhh...eeeee..........eeeee.hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...........eeeeehhhhh...hhhhhhhhhhhhhhhhhhhee.eeehhhhhh..............eeeee......hhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------BETA_ELIM_LYASE    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vlf A   1 MNYPAEPFRIKSVETVSMIPRDERLKKMQEAGYNTFLLNSKDIYIDLLTDSGTNAMSDKQWAGMMMGDEAYAGSENFYHLERTVQELFGFKHIVPTHQGRGAENLLSQLAIKPGQYVAGNMYFTTTRYHQEKNGAVFVDIVRDEAHDAGLNIAFKGDIDLKKLQKLIDEKGAENIAYICLAVTVNLAGGQPVSMANMRAVRELTEAHGIKVFYDATRCVENAYFIKEQEQGFENKSIAEIVHEMFSYADGCTMSGKKDCLVNIGGFLCMNDDEMFSSAKELVVVYEGMPSYGGLAGRDMEAMAIGLREAMQYEYIEHRVKQVRYLGDKLKAAGVPIVEPVGGHAVFLDARRFCEHLTQDEFPAQSLAASIYVETGVRSMERGIISAGRNNVTGEHHRPKLETVRLTIPRRVYTYAHMDVVADGIIKLYQHKEDIRGLKFIYEPKQLRFFTARFDYI 456
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450

Chain B from PDB  Type:PROTEIN  Length:456
 aligned with TPL_CITFR | P31013 from UniProtKB/Swiss-Prot  Length:456

    Alignment length:456
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450      
            TPL_CITFR     1 MNYPAEPFRIKSVETVSMIPRDERLKKMQEAGYNTFLLNSKDIYIDLLTDSGTNAMSDKQWAGMMMGDEAYAGSENFYHLERTVQELFGFKHIVPTHQGRGAENLLSQLAIKPGQYVAGNMYFTTTRYHQEKNGAVFVDIVRDEAHDAGLNIAFKGDIDLKKLQKLIDEKGAENIAYICLAVTVNLAGGQPVSMANMRAVRELTEAHGIKVFYDATRCVENAYFIKEQEQGFENKSIAEIVHEMFSYADGCTMSGKKDCLVNIGGFLCMNDDEMFSSAKELVVVYEGMPSYGGLAGRDMEAMAIGLREAMQYEYIEHRVKQVRYLGDKLKAAGVPIVEPVGGHAVFLDARRFCEHLTQDEFPAQSLAASIYVETGVRSMERGIISAGRNNVTGEHHRPKLETVRLTIPRRVYTYAHMDVVADGIIKLYQHKEDIRGLKFIYEPKQLRFFTARFDYI 456
               SCOP domains d2vlfb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2vlfB01 B:1-57,B:311-455                                 2vlfB02 B:58-310 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                         2vlfB01 B:1-57,B:311-455 Aspartate Aminotransferase, domain 1                                                                                    - CATH domains
           Pfam domains (1) ---------------------------------------------Beta_elim_lyase-2vlfB01 B:46-423                                                                                                                                                                                                                                                                                                                                                          --------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------Beta_elim_lyase-2vlfB02 B:46-423                                                                                                                                                                                                                                                                                                                                                          --------------------------------- Pfam domains (2)
         Sec.struct. author ...................hhhhhhhhhhhh..hhhhhhhhhh.eee.........hhhhhhhhh........hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeee...hhhhhhhhhhh..eeee..hhhhhh...........hhhhhhhhhhhhh...eeeeeee...........hhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh......hhhhhhhhhhhh..eeeee..........eeeee.hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeeehhhhh...hhhhhhhhhhhhhhhhhhheeeeeehhhhhh..............eeeee......hhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhheeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------BETA_ELIM_LYASE    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vlf B   1 MNYPAEPFRIKSVETVSMIPRDERLKKMQEAGYNTFLLNSKDIYIDLLTDSGTNAMSDKQWAGMMMGDEAYAGSENFYHLERTVQELFGFKHIVPTHQGRGAENLLSQLAIKPGQYVAGNMYFTTTRYHQEKNGAVFVDIVRDEAHDAGLNIAFKGDIDLKKLQKLIDEKGAENIAYICLAVTVNLAGGQPVSMANMRAVRELTEAHGIKVFYDATRCVENAYFIKEQEQGFENKSIAEIVHEMFSYADGCTMSGKKDCLVNIGGFLCMNDDEMFSSAKELVVVYEGMPSYGGLAGRDMEAMAIGLREAMQYEYIEHRVKQVRYLGDKLKAAGVPIVEPVGGHAVFLDARRFCEHLTQDEFPAQSLAASIYVETGVRSMERGIISAGRNNVTGEHHRPKLETVRLTIPRRVYTYAHMDVVADGIIKLYQHKEDIRGLKFIYEPKQLRFFTARFDYI 456
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450

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: Beta-eliminating lyases (16)

Protein domain: automated matches (8)

Citrobacter freundii [TaxId: 546] (8)

1a	d2vlfa_	A:
1b	d2vlfb_	B:

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PLP_aminotran (240)

Family: Beta_elim_lyase (13)

Citrobacter freundii (3)

1a	Beta_elim_lyase-2vlfB01	B:46-423
1b	Beta_elim_lyase-2vlfB02	B:46-423

Asymmetric Unit(hide GO term definitions)

Chain A,B (TPL_CITFR | P31013)

molecular function
	GO:0016830	carbon-carbon lyase activity	Catalysis of the cleavage of C-C bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond.
	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:0050371	tyrosine phenol-lyase activity	Catalysis of the reaction: L-tyrosine + H(2)O = NH(4)(+) + phenol + pyruvate.
biological process
	GO:0009072	aromatic amino acid family metabolic process	The chemical reactions and pathways involving aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
	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:0006570	tyrosine metabolic process	The chemical reactions and pathways involving tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid.

Asymmetric Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
		K	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		P33	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		AC5	[ RasMol ]	+environment [ RasMol ]
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	Cis Peptide Bonds
		Glu A:338 - Pro A:339	[ RasMol ]
		Glu B:338 - Pro B:339	[ RasMol ]
		Val A:182 - Thr A:183	[ RasMol ]
		Val B:182 - Thr B:183	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Access by PDB/NDB ID
	2vlf
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
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		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
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Access by UniProt ID/Accession number
	TPL_CITFR \| P31013
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	4.1.99.2
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	(no 'MIM ID' available)
		Disease Information	:	OMIM

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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Access by UniProt ID/Accession number
	TPL_CITFR \| P31013
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	TPL_CITFR \| P31013	:	1tpl 2ez1 2ez2 2tpl 2vlh 2ycn 2ycp 2yct 2yhk

1tpl	TYROSINE PHENOL-LYASE
2ez1	HOLO TYROSINE PHENOL-LYASE FROM CITROBACTER FREUNDII AT PH8.0
2ez2	APO TYROSINE PHENOL-LYASE FROM CITROBACTER FREUNDII AT PH8.0
2tpl	TYROSINE PHENOL-LYASE FROM CITROBACTER INTERMEDIUS COMPLEX WITH 3-(4'-HYDROXYPHENYL) PROPIONIC ACID, PYRIDOXAL-5'-PHOSPHATE AND CS+ ION
2vlh	QUINONOID INTERMEDIATE OF CITROBACTER FREUNDII TYROSINE PHENOL-LYASE FORMED WITH METHIONINE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (2, 4)

Pfam Domains (1, 2)

Gene Ontology (7, 7)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File