1W27 - JenaLib

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Title :   PHENYLALANINE AMMONIA-LYASE (PAL) FROM PETROSELINUM CRISPUM

Authors :   H. Ritter, G. E. Schulz

Date :   29 Jun 04 (Deposition) - 25 Nov 04 (Release) - 16 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Lyase, Phenylpropanoid Metabolism, Mio (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Ritter, G. E. Schulz
Structural Basis For The Entrance Into The Phenylpropanoid Metabolism Catalyzed By Phenylalanine Ammonia-Lyase
Plant Cell V. 16 3426 2004
PubMed-ID: 15548745 | Reference-DOI: 10.1105/TPC.104.025288

Molecule 1 - PHENYLALANINE AMMONIA-LYASE 1
	Chains	:	A, B
	EC Number	:	4.3.1.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PT7-7
	Organism Common	:	PARSLEY
	Organism Scientific	:	PETROSELINUM CRISPUM
	Organism Taxid	:	4043
	Other Details	:	SYNTHETIC GENE

		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	DTT	2	Ligand/Ion	2,3-DIHYDROXY-1,4-DITHIOBUTANE
2	MDO	2	Mod. Amino Acid	{2-[(1S)-1-AMINOETHYL]-5-HYDROXY-4-METHYL-1H-IMIDAZOL-1-YL}ACETIC ACID

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	DTT	4	Ligand/Ion	2,3-DIHYDROXY-1,4-DITHIOBUTANE
2	MDO	4	Mod. Amino Acid	{2-[(1S)-1-AMINOETHYL]-5-HYDROXY-4-METHYL-1H-IMIDAZOL-1-YL}ACETIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:137 , MDO A:203 , LEU A:206 , ASN A:260 , HOH A:2240 , HOH A:2386 , HOH A:2533 , HOH A:2534	BINDING SITE FOR RESIDUE DTT A1717
2	AC2	SOFTWARE	PHE B:137 , MDO B:203 , LEU B:206 , ASN B:260 , HOH B:2392 , HOH B:2400 , HOH B:2537	BINDING SITE FOR RESIDUE DTT B1717

(no "SS Bond" information available for 1W27)

Asymmetric Unit

No.	Residues
1	Asn A:384	-	Pro A:385
2	His A:557	-	Pro A:558
3	Asn B:384	-	Pro B:385
4	His B:557	-	Pro B:558

(no "SAP(SNP)/Variant" information available for 1W27)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PAL_HISTIDASE	PS00488	Phenylalanine and histidine ammonia-lyases signature.	PAL1_PETCR	198-214	2	A:198-214 B:198-214

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PAL_HISTIDASE	PS00488	Phenylalanine and histidine ammonia-lyases signature.	PAL1_PETCR	198-214	4	A:198-214 B:198-214

(no "Exon" information available for 1W27)

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:690
 aligned with PAL1_PETCR | P24481 from UniProtKB/Swiss-Prot  Length:716

    Alignment length:692
                                    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       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714  
           PAL1_PETCR    25 EDPLYWGIAAEAMTGSHLDEVKKMVAEYRKPVVKLGGETLTISQVAAISARDGSGVTVELSEAARAGVKASSDWVMDSMNKGTDSYGVTTGFGATSHRRTKQGGALQKELIRFLNAGIFGNGSDNTLPHSATRAAMLVRINTLLQGYSGIRFEILEAITKFLNQNITPCLPLRGTITASGDLVPLSYIAGLLTGRPNSKAVGPTGVILSPEEAFKLAGVEGGFFELQPKEGLALVNGTAVGSGMASMVLFEANILAVLAEVMSAIFAEVMQGKPEFTDHLTHKLKHHPGQIEAAAIMEHILDGSAYVKAAQKLHEMDPLQKPKQDRYALRTSPQWLGPQIEVIRSSTKMIEREINSVNDNPLIDVSRNKAIHGGNFQGTPIGVSMDNTRLAIAAIGKLMFAQFSELVNDFYNNGLPSNLSGGRNPSLDYGFKGAEIAMASYCSELQFLANPVTNHVQSAEQHNQDVNSLGLISSRKTSEAVEILKLMSTTFLVGLCQAIDLRHLEENLKSTVKNTVSSVAKRVLTMGVNGELHPSRFCEKDLLRVVDREYIFAYIDDPCSATYPLMQKLRQTLVEHALKNGDNERNLSTSIFQKIATFEDELKALLPKEVESARAALESGNPAIPNRIEECRSYPLYKFVRKELGTEYLTGEKVTSPGEEFEKVFIAMSKGEIIDPLLECLESWNGAPLPIC 716
               SCOP domains d1w27a_ A: Phenylalanine ammonia-lyase, PAL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1w27A01 A:25-262 Fumarase/aspartase (N-terminal domain)                                                                                                                                                                                       1w27A02 A:263-528,A:651-716 Fumarase/aspartase (Central domain)                                                                                                                                                                                                           1w27A03 A:529-650 Phenylalanine ammonia-lyase 1; domain 3                                                                 1w27A02 A:263-528,A:651-716 Fumarase/aspartase (Central domain)    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhh....hhhhhhhhhhhh...eeee......hhhhhhhh.......eeee....hhhhhhhhhhhhhhh.........................hhhhhhhhhh..........eee.hhhhhhhhhhhhhh.........hhhhhhhhhhhh..eeeeeee.....-.-.hhhhhhhhhhhh.....eeee...eeeehhhhhhhh............hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhh...hhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeee..eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh...............hhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhh..............hhhhhhhhhhhhhh..hhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------PAL_HISTIDASE    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w27 A  25 EDPLYWGIAAEAMTGSHLDEVKKMVAEYRKPVVKLGGETLTISQVAAISARDGSGVTVELSEAARAGVKASSDWVMDSMNKGTDSYGVTTGFGATSHRRTKQGGALQKELIRFLNAGIFGNGSDNTLPHSATRAAMLVRINTLLQGYSGIRFEILEAITKFLNQNITPCLPLRGTIT-a-DLVPLSYIAGLLTGRPNSKAVGPTGVILSPEEAFKLAGVEGGFFELQPKEGLALVNGTAVGSGMASMVLFEANILAVLAEVMSAIFAEVMQGKPEFTDHLTHKLKHHPGQIEAAAIMEHILDGSAYVKAAQKLHEMDPLQKPKQDRYALRTSPQWLGPQIEVIRSSTKMIEREINSVNDNPLIDVSRNKAIHGGNFQGTPIGVSMDNTRLAIAAIGKLMFAQFSELVNDFYNNGLPSNLSGGRNPSLDYGFKGAEIAMASYCSELQFLANPVTNHVQSAEQHNQDVNSLGLISSRKTSEAVEILKLMSTTFLVGLCQAIDLRHLEENLKSTVKNTVSSVAKRVLTMGVNGELHPSRFCEKDLLRVVDREYIFAYIDDPCSATYPLMQKLRQTLVEHALKNGDNERNLSTSIFQKIATFEDELKALLPKEVESARAALESGNPAIPNRIEECRSYPLYKFVRKELGTEYLTGEKVTSPGEEFEKVFIAMSKGEIIDPLLECLESWNGAPLPIC 716
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194      | |-|      214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714  
                                                                                                                                                                                                          201 | |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                                                                                                                                                                                                            203-MDO                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
                                                                                                                                                                                                              205

Chain B from PDB  Type:PROTEIN  Length:690
 aligned with PAL1_PETCR | P24481 from UniProtKB/Swiss-Prot  Length:716

    Alignment length:692
                                    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       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714  
           PAL1_PETCR    25 EDPLYWGIAAEAMTGSHLDEVKKMVAEYRKPVVKLGGETLTISQVAAISARDGSGVTVELSEAARAGVKASSDWVMDSMNKGTDSYGVTTGFGATSHRRTKQGGALQKELIRFLNAGIFGNGSDNTLPHSATRAAMLVRINTLLQGYSGIRFEILEAITKFLNQNITPCLPLRGTITASGDLVPLSYIAGLLTGRPNSKAVGPTGVILSPEEAFKLAGVEGGFFELQPKEGLALVNGTAVGSGMASMVLFEANILAVLAEVMSAIFAEVMQGKPEFTDHLTHKLKHHPGQIEAAAIMEHILDGSAYVKAAQKLHEMDPLQKPKQDRYALRTSPQWLGPQIEVIRSSTKMIEREINSVNDNPLIDVSRNKAIHGGNFQGTPIGVSMDNTRLAIAAIGKLMFAQFSELVNDFYNNGLPSNLSGGRNPSLDYGFKGAEIAMASYCSELQFLANPVTNHVQSAEQHNQDVNSLGLISSRKTSEAVEILKLMSTTFLVGLCQAIDLRHLEENLKSTVKNTVSSVAKRVLTMGVNGELHPSRFCEKDLLRVVDREYIFAYIDDPCSATYPLMQKLRQTLVEHALKNGDNERNLSTSIFQKIATFEDELKALLPKEVESARAALESGNPAIPNRIEECRSYPLYKFVRKELGTEYLTGEKVTSPGEEFEKVFIAMSKGEIIDPLLECLESWNGAPLPIC 716
               SCOP domains d1w27b_ B: Phenylalanine ammonia-lyase, PAL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1w27B01 B:25-262 Fumarase/aspartase (N-terminal domain)                                                                                                                                                                                       1w27B02 B:263-528,B:651-716 Fumarase/aspartase (Central domain)                                                                                                                                                                                                           1w27B03 B:529-650 Phenylalanine ammonia-lyase 1; domain 3                                                                 1w27B02 B:263-528,B:651-716 Fumarase/aspartase (Central domain)    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhh....hhhhhhhhhhhh...eeee......hhhhhhhh.......eeee....hhhhhhhhhhhhhhh.........................hhhhhhhhhh..........eee.hhhhhhhhhhhhhh.........hhhhhhhhhhhh..eeeeeee.....-.-.hhhhhhhhhhhh.....eeee...eeeehhhhhhhh............hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhh...hhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeee..eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh...............hhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhh..............hhhhhhhhhhhhhh..hhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------PAL_HISTIDASE    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w27 B  25 EDPLYWGIAAEAMTGSHLDEVKKMVAEYRKPVVKLGGETLTISQVAAISARDGSGVTVELSEAARAGVKASSDWVMDSMNKGTDSYGVTTGFGATSHRRTKQGGALQKELIRFLNAGIFGNGSDNTLPHSATRAAMLVRINTLLQGYSGIRFEILEAITKFLNQNITPCLPLRGTIT-a-DLVPLSYIAGLLTGRPNSKAVGPTGVILSPEEAFKLAGVEGGFFELQPKEGLALVNGTAVGSGMASMVLFEANILAVLAEVMSAIFAEVMQGKPEFTDHLTHKLKHHPGQIEAAAIMEHILDGSAYVKAAQKLHEMDPLQKPKQDRYALRTSPQWLGPQIEVIRSSTKMIEREINSVNDNPLIDVSRNKAIHGGNFQGTPIGVSMDNTRLAIAAIGKLMFAQFSELVNDFYNNGLPSNLSGGRNPSLDYGFKGAEIAMASYCSELQFLANPVTNHVQSAEQHNQDVNSLGLISSRKTSEAVEILKLMSTTFLVGLCQAIDLRHLEENLKSTVKNTVSSVAKRVLTMGVNGELHPSRFCEKDLLRVVDREYIFAYIDDPCSATYPLMQKLRQTLVEHALKNGDNERNLSTSIFQKIATFEDELKALLPKEVESARAALESGNPAIPNRIEECRSYPLYKFVRKELGTEYLTGEKVTSPGEEFEKVFIAMSKGEIIDPLLECLESWNGAPLPIC 716
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194      | |-|      214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714  
                                                                                                                                                                                                          201 | |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                                                                                                                                                                                                            203-MDO                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
                                                                                                                                                                                                              205

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: All alpha proteins (14657)

Fold: L-aspartase-like (67)

Superfamily: L-aspartase-like (67)

Family: HAL/PAL-like (10)

Protein domain: Phenylalanine ammonia-lyase, PAL (4)

Parsley (Petroselinum crispum), PAL1 [TaxId: 4043] (1)

1a	d1w27a_	A:
1b	d1w27b_	B:

(no "Pfam Domain" information available for 1W27)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PAL1_PETCR | P24481)

molecular function
	GO:0016841	ammonia-lyase activity	Catalysis of the release of ammonia by the cleavage of a carbon-nitrogen bond or the reverse reaction with ammonia as a substrate.
	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:0045548	phenylalanine ammonia-lyase activity	Catalysis of the reaction: L-phenylalanine = NH(4)(+) + trans-cinnamate.
biological process
	GO:0006559	L-phenylalanine catabolic process	The chemical reactions and pathways resulting in the breakdown of phenylalanine, 2-amino-3-phenylpropanoic acid.
	GO:0009800	cinnamic acid biosynthetic process	The chemical reactions and pathways resulting in the formation of cinnamic acid, 3-phenyl-2-propenoic acid.
	GO:0009698	phenylpropanoid metabolic process	The chemical reactions and pathways involving aromatic derivatives of trans-cinnamic acid.
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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	Cis Peptide Bonds
		Asn A:384 - Pro A:385	[ RasMol ]
		Asn B:384 - Pro B:385	[ RasMol ]
		His A:557 - Pro A:558	[ RasMol ]
		His B:557 - Pro B:558	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	1w27
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Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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Exons (0, 0)

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