2YHK - JenaLib

Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   D214A MUTANT OF TYROSINE PHENOL-LYASE FROM CITROBACTER FREUNDII

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

Date :   03 May 11 (Deposition) - 02 May 12 (Release) - 28 Nov 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.91

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

Keywords :   Lyase, Pyridoxal-5'-Phosphate-Dependent Enzyme, Beta-Elimination Reaction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Milic, T. V. Demidkina, L. N. Zakomirdina, D. Matkovic-Calogovic, A. A. Antson
Crystal Structure Of Citrobacter Freundii Asp214Ala Tyrosin Phenol-Lyase Reveals That Asp214 Is Critical For Maintainin A Strain In The Internal Aldimine
Croatica Chemica Acta V. 85 283 2012
PubMed: search | Reference-DOI: 10.5562/CCA1915

Molecule 1 - TYROSINE PHENOL-LYASE
	Atcc	:	13316
	Chains	:	A, B
	EC Number	:	4.1.99.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTZTPLD214A
	Expression System Strain	:	SVS 370
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	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 (5, 12)

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	PEG	6	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL
5	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Biological Unit 1 (4, 20)

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	PEG	12	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PG4	2	Ligand/Ion	TETRAETHYLENE GLYCOL
5	PLP	4	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:52 , ASN A:262 , HOH A:2082 , HOH A:2263 , GLU B:69 , HOH B:2246	BINDING SITE FOR RESIDUE K A 500
02	AC2	SOFTWARE	LYS A:132 , ASN A:133 , TYR A:285 , HOH A:2181 , GLN B:108 , LYS B:132 , ASN B:133 , TYR B:285	BINDING SITE FOR RESIDUE PG4 A 600
03	AC3	SOFTWARE	LEU A:109 , ILE A:111 , HOH A:2384	BINDING SITE FOR RESIDUE PEG A 601
04	AC4	SOFTWARE	LEU A:186 , ARG A:381 , LEU A:400 , THR A:402 , HOH A:2170	BINDING SITE FOR RESIDUE PEG A 603
05	AC5	SOFTWARE	LYS A:226 , TYR A:312 , HOH A:2385	BINDING SITE FOR RESIDUE PEG A 604
06	AC6	SOFTWARE	GLN A:98 , GLY A:99 , ARG A:100 , PHE A:123 , ASN A:185 , THR A:216 , ARG A:217 , SER A:254 , LYS A:257 , HOH A:2083 , HOH A:2149	BINDING SITE FOR RESIDUE PLP A1257
07	AC7	SOFTWARE	GLU A:69 , HOH A:2103 , HOH A:2283 , GLY B:52 , ASN B:262	BINDING SITE FOR RESIDUE K B 500
08	AC8	SOFTWARE	TYR A:3 , TYR A:324 , TYR A:414 , ASP A:418 , HOH A:2357 , TYR B:3 , ALA B:415 , ASP B:418 , HOH B:2004	BINDING SITE FOR RESIDUE P33 B 600
09	AC9	SOFTWARE	LEU B:109 , ILE B:111 , LYS B:112	BINDING SITE FOR RESIDUE PEG B 601
10	BC1	SOFTWARE	HOH A:2108 , GLN B:98 , GLY B:99 , ARG B:100 , PHE B:123 , ASN B:185 , THR B:216 , ARG B:217 , SER B:254 , LYS B:257 , HOH B:2127	BINDING SITE FOR RESIDUE PLP B1257

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

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 2YHK)

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 2YHK)

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:455
 aligned with TPL_CITFR | P31013 from UniProtKB/Swiss-Prot  Length:456

    Alignment length:455
                                    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       401       411       421       431       441       451     
            TPL_CITFR     2 NYPAEPFRIKSVETVSMIPRDERLKKMQEAGYNTFLLNSKDIYIDLLTDSGTNAMSDKQWAGMMMGDEAYAGSENFYHLERTVQELFGFKHIVPTHQGRGAENLLSQLAIKPGQYVAGNMYFTTTRYHQEKNGAVFVDIVRDEAHDAGLNIAFKGDIDLKKLQKLIDEKGAENIAYICLAVTVNLAGGQPVSMANMRAVRELTEAHGIKVFYDATRCVENAYFIKEQEQGFENKSIAEIVHEMFSYADGCTMSGKKDCLVNIGGFLCMNDDEMFSSAKELVVVYEGMPSYGGLAGRDMEAMAIGLREAMQYEYIEHRVKQVRYLGDKLKAAGVPIVEPVGGHAVFLDARRFCEHLTQDEFPAQSLAASIYVETGVRSMERGIISAGRNNVTGEHHRPKLETVRLTIPRRVYTYAHMDVVADGIIKLYQHKEDIRGLKFIYEPKQLRFFTARFDYI 456
               SCOP domains d2yhka_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhh..hhhhhhhhhh.eee.........hhhhhhhhh........hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeee...hhhhhhhhhhh..eeee..hhhhhh...........hhhhhhhhhhhhh...eeeeeee...........hhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh......hhhhhhhhhhh...eeeee..........eeeee.hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeeehhhhh...hhhhhhhhhhhhhhhhhhheeeeeehhhhhh..............eeeee......hhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhheeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------BETA_ELIM_LYASE    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yhk A   2 NYPAEPFRIKSVETVSMIPRDERLKKMQEAGYNTFLLNSKDIYIDLLTDSGTNAMSDKQWAGMMMGDEAYAGSENFYHLERTVQELFGFKHIVPTHQGRGAENLLSQLAIKPGQYVAGNMYFTTTRYHQEKNGAVFVDIVRDEAHDAGLNIAFKGDIDLKKLQKLIDEKGAENIAYICLAVTVNLAGGQPVSMANMRAVRELTEAHGIKVFYAATRCVENAYFIKEQEQGFENKSIAEIVHEMFSYADGCTMSGKKDCLVNIGGFLCMNDDEMFSSAKELVVVYEGMPSYGGLAGRDMEAMAIGLREAMQYEYIEHRVKQVRYLGDKLKAAGVPIVEPVGGHAVFLDARRFCEHLTQDEFPAQSLAASIYVETGVRSMERGIISAGRNNVTGEHHRPKLETVRLTIPRRVYTYAHMDVVADGIIKLYQHKEDIRGLKFIYEPKQLRFFTARFDYI 456
                                    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       401       411       421       431       441       451

Chain B from PDB  Type:PROTEIN  Length:455
 aligned with TPL_CITFR | P31013 from UniProtKB/Swiss-Prot  Length:456

    Alignment length:455
                                    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       401       411       421       431       441       451     
            TPL_CITFR     2 NYPAEPFRIKSVETVSMIPRDERLKKMQEAGYNTFLLNSKDIYIDLLTDSGTNAMSDKQWAGMMMGDEAYAGSENFYHLERTVQELFGFKHIVPTHQGRGAENLLSQLAIKPGQYVAGNMYFTTTRYHQEKNGAVFVDIVRDEAHDAGLNIAFKGDIDLKKLQKLIDEKGAENIAYICLAVTVNLAGGQPVSMANMRAVRELTEAHGIKVFYDATRCVENAYFIKEQEQGFENKSIAEIVHEMFSYADGCTMSGKKDCLVNIGGFLCMNDDEMFSSAKELVVVYEGMPSYGGLAGRDMEAMAIGLREAMQYEYIEHRVKQVRYLGDKLKAAGVPIVEPVGGHAVFLDARRFCEHLTQDEFPAQSLAASIYVETGVRSMERGIISAGRNNVTGEHHRPKLETVRLTIPRRVYTYAHMDVVADGIIKLYQHKEDIRGLKFIYEPKQLRFFTARFDYI 456
               SCOP domains d2yhkb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhh..hhhhhhhhhh.ee..........hhhhhhhhh........hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeee...hhhhhhhhhhh..eeee..hhhhhh...........hhhhhhhhhhhhh...eeeeeee...........hhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh......hhhhhhhhhhh...eeeee..........eeeee.hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeeehhhhh...hhhhhhhhhhhhhhhhhhhee.eeehhhhhh..............eeeee......hhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhheeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------BETA_ELIM_LYASE    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yhk B   2 NYPAEPFRIKSVETVSMIPRDERLKKMQEAGYNTFLLNSKDIYIDLLTDSGTNAMSDKQWAGMMMGDEAYAGSENFYHLERTVQELFGFKHIVPTHQGRGAENLLSQLAIKPGQYVAGNMYFTTTRYHQEKNGAVFVDIVRDEAHDAGLNIAFKGDIDLKKLQKLIDEKGAENIAYICLAVTVNLAGGQPVSMANMRAVRELTEAHGIKVFYAATRCVENAYFIKEQEQGFENKSIAEIVHEMFSYADGCTMSGKKDCLVNIGGFLCMNDDEMFSSAKELVVVYEGMPSYGGLAGRDMEAMAIGLREAMQYEYIEHRVKQVRYLGDKLKAAGVPIVEPVGGHAVFLDARRFCEHLTQDEFPAQSLAASIYVETGVRSMERGIISAGRNNVTGEHHRPKLETVRLTIPRRVYTYAHMDVVADGIIKLYQHKEDIRGLKFIYEPKQLRFFTARFDYI 456
                                    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       401       411       421       431       441       451

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	d2yhka_	A:
1b	d2yhkb_	B:

(no "CATH Domain" information available for 2YHK)

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

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
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	Ligands, Modified Residues, Ions
		K	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		P33	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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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
	2yhk
		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)
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Access by UniProt ID/Accession number
	TPL_CITFR \| P31013
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	4.1.99.2
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		Disease Information	:	OMIM

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	TPL_CITFR \| P31013
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UniProtKB/Swiss-Prot
	TPL_CITFR \| P31013	:	1tpl 2ez1 2ez2 2tpl 2vlf 2vlh 2ycn 2ycp 2yct

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
2vlf	QUINONOID INTERMEDIATE OF CITROBACTER FREUNDII TYROSINE PHENOL-LYASE FORMED WITH ALANINE
2vlh	QUINONOID INTERMEDIATE OF CITROBACTER FREUNDII TYROSINE PHENOL-LYASE FORMED WITH METHIONINE
2ycn	Y71F MUTANT OF TYROSINE PHENOL-LYASE FROM CITROBACTER FREUNDII IN COMPLEX WITH QUINONOID INTERMEDIATE FORMED WITH 3-FLUORO-L-TYROSINE
2ycp	F448H MUTANT OF TYROSINE PHENOL-LYASE FROM CITROBACTER FREUNDII IN COMPLEX WITH QUINONOID INTERMEDIATE FORMED WITH 3-FLUORO-L-TYROSINE
2yct	TYROSINE PHENOL-LYASE FROM CITROBACTER FREUNDII IN COMPLEX WITH PYRIDINE N-OXIDE AND THE QUINONOID INTERMEDIATE FORMED WITH L-ALANINE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 12)

Sites (10, 10)

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 (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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