1T6J - JenaLib

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Title :   CRYSTAL STRUCTURE OF PHENYLALANINE AMMONIA LYASE FROM RHODOSPORIDIUM TORULOIDES

Authors :   J. C. Calabrese, D. B. Jordan

Date :   06 May 04 (Deposition) - 12 Oct 04 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Triple Helix Coiled Coil; Mio; Cinnamate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. C. Calabrese, D. B. Jordan, A. Boodhoo, S. Sariaslani, T. Vannelli
Crystal Structure Of Phenylalanine Ammonia Lyase: Multiple Helix Dipoles Implicated In Catalysis.
Biochemistry V. 43 11403 2004
PubMed-ID: 15350127 | Reference-DOI: 10.1021/BI049053+

Molecule 1 - PHENYLALANINE AMMONIA-LYASE
	Chains	:	A, B
	EC Number	:	4.3.1.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-24A PEAL
	Expression System Strain	:	B834(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PAL
	Organism Scientific	:	RHODOSPORIDIUM TORULOIDES
	Organism Taxid	:	5286

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 29)

No.	Name	Count	Type	Full Name
1	175	2	Mod. Amino Acid	3,5-DIHYDRO-5-METHYLIDENE-4H-IMIDAZOL-4-ON
2	CIN	1	Ligand/Ion	4-CARBOXYCINNAMIC ACID
3	MSE	26	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (3, 58)

No.	Name	Count	Type	Full Name
1	175	4	Mod. Amino Acid	3,5-DIHYDRO-5-METHYLIDENE-4H-IMIDAZOL-4-ON
2	CIN	2	Ligand/Ion	4-CARBOXYCINNAMIC ACID
3	MSE	52	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	175 B:211 , LEU B:266 , ASN B:397 , LYS B:468 , GLU B:496 , GLN B:500	BINDING SITE FOR RESIDUE CIN B 1001

(no "SS Bond" information available for 1T6J)

Asymmetric Unit

No.	Residues
1	Asn A:397	-	Pro A:398
2	Asn B:397	-	Pro B:398

(no "SAP(SNP)/Variant" information available for 1T6J)

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.	PALY_RHOTO	207-223	2	A:207-223 B:207-223

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.	PALY_RHOTO	207-223	4	A:207-223 B:207-223

(no "Exon" information available for 1T6J)

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:647
 aligned with PALY_RHOTO | P11544 from UniProtKB/Swiss-Prot  Length:716

    Alignment length:678
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708        
           PALY_RHOTO    39 TTQVTQVDIVEKMLAAPTDSTLELDGYSLNLGDVVSAARKGRPVRVKDSDEIRSKIDKSVEFLRSQLSMSVYGVTTGFGGSADTRTEDAISLQKALLEHQLCGVLPSSFDSFRLGRGLENSLPLEVVRGAMTIRVNSLTRGHSAVRLVVLEALTNFLNHGITPIVPLRGTISASGDLSPLSYIAAAISGHPDSKVHVVHEGKEKILYAREAMALFNLEPVVLGPKEGLGLVNGTAVSASMATLALHDAHMLSLLSQSLTAMTVEAMVGHAGSFHPFLHDVTRPHPTQIEVAGNIRKLLEGSRFAVHHEEEVKVKDDEGILRQDRYPLRTSPQWLGPLVSDLIHAHAVLTIEAGQSTTDNPLIDVENKTSHHGGNFQAAAVANTMEKTRLGLAQIGKLNFTQLTEMLNAGMNRGLPSCLAAEDPSLSYHCKGLDIAAAAYTSELGHLANPVTTHVQPAEMANQAVNSLALISARRTTESNDVLSLLLATHLYCVLQAIDLRAIEFEFKKQFGPAIVSLIDQHFGSAMTGSNLRDELVEKVNKTLAKRLEQTNSYDLVPRWHDAFSFAAGTVVEVLSSTSLSLAAVNAWKVAAAESAISLTRQVRETFWSAASTSSPALSYLSPRTQILYAFVREELGVKARRGDVFLGKQEVTIGSNVSKIYEAIKSGRINNVLLKMLA 716
               SCOP domains d1t6ja_ A: Phenylalanine ammonia-lyase, PAL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1t6jA01 A:39-271 Fumarase/aspartase (N-terminal domain)                                                                                                                                                                                  1t6jA02 A:272-545,A:649-716 Fumarase/aspartase (Central domain)                                                                                                                                                                                                                   -------------------------------------------------------------------------------------------------------1t6jA02 A:272-545,A:649-716 Fumarase/aspartase (Central domain)      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh.....eee.....hhhhhhhhhhh...eee...hhhhhhhhhhhhhhhh.-------------------.hhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..ee..........--hhhhhhhhhhhhh.....eeeeee..eeeeeehhhhhhhh...........hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhhhh...........----------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee.hhhh.ee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhh..hhhhhhhhhhhhhhhhhhh..hhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh........hhhhhh....hhhhhhhhhhhhhhhh.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------PAL_HISTIDASE    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1t6j A  39 TTQVTQVDIVEKmLAAPTDSTLELDGYSLNLGDVVSAARKGRPVRVKDSDEIRSKIDKSVEFLRSQ-------------------TEDAISLQKALLEHQLCGVLPSSFDSFRLGRGLENSLPLEVVRGAmTIRVNSLTRGHSAVRLVVLEALTNFLNHGITPIVPLRGTISa--DLSPLSYIAAAISGHPDSKVHVVHEGKEKILYAREAmALFNLEPVVLGPKEGLGLVNGTAVSASmATLALHDAHmLSLLSQSLTAmTVEAmVGHAGSFHPFLHDVTRPHPTQIEVAGNIRKLLEGSRFAVHHEEE----------RQDRYPLRTSPQWLGPLVSDLIHAHAVLTIEAGQSTTDNPLIDVENKTSHHGGNFQAAAVANTmEKTRLGLAQIGKLNFTQLTEmLNAGmNRGLPSCLAAEDPSLSYHCKGLDIAAAAYTSELGHLANPVTTHVQPAEmANQAVNSLALISARRTTESNDVLSLLLATHLYCVLQAIDLRAIEFEFKKQFGPAIVSLIDQHFGSAmTGSNLRDELVEKVNKTLAKRLEQTNSYDLVPRWHDAFSFAAGTVVEVLSSTSLSLAAVNAWKVAAAESAISLTRQVRETFWSAASTSSPALSYLSPRTQILYAFVREELGVKARRGDVFLGKQEVTIGSNVSKIYEAIKSGRINNVLLKmLA 716
                                    48  |     58        68        78        88        98     |   -         -     | 128       138       148       158       168|      178       188       198       208  |  | 218       228       238       248 |     258       268       278       288       298|    | 308       318       328       338       348         -|      368       378       388       398       408       418   |   428       438    |  448       458       468       478       488       498       508       518       528       538       548       558     | 568       578       588       598       608       618       628       638       648       658       668       678       688       698       708     |  
                                       51-MSE                                              104                 124                                          169-MSE                                   211-175                                250-MSE                     278-MSE   288-MSE    299-MSE|                                         348        359                                                            422-MSE              443-MSE|                                              497-MSE                                                            564-MSE                                                                                                                                               714-MSE
                                                                                                                                                                                                         214                                                                                       304-MSE                                                                                                                                         448-MSE

Chain B from PDB  Type:PROTEIN  Length:647
 aligned with PALY_RHOTO | P11544 from UniProtKB/Swiss-Prot  Length:716

    Alignment length:678
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708        
           PALY_RHOTO    39 TTQVTQVDIVEKMLAAPTDSTLELDGYSLNLGDVVSAARKGRPVRVKDSDEIRSKIDKSVEFLRSQLSMSVYGVTTGFGGSADTRTEDAISLQKALLEHQLCGVLPSSFDSFRLGRGLENSLPLEVVRGAMTIRVNSLTRGHSAVRLVVLEALTNFLNHGITPIVPLRGTISASGDLSPLSYIAAAISGHPDSKVHVVHEGKEKILYAREAMALFNLEPVVLGPKEGLGLVNGTAVSASMATLALHDAHMLSLLSQSLTAMTVEAMVGHAGSFHPFLHDVTRPHPTQIEVAGNIRKLLEGSRFAVHHEEEVKVKDDEGILRQDRYPLRTSPQWLGPLVSDLIHAHAVLTIEAGQSTTDNPLIDVENKTSHHGGNFQAAAVANTMEKTRLGLAQIGKLNFTQLTEMLNAGMNRGLPSCLAAEDPSLSYHCKGLDIAAAAYTSELGHLANPVTTHVQPAEMANQAVNSLALISARRTTESNDVLSLLLATHLYCVLQAIDLRAIEFEFKKQFGPAIVSLIDQHFGSAMTGSNLRDELVEKVNKTLAKRLEQTNSYDLVPRWHDAFSFAAGTVVEVLSSTSLSLAAVNAWKVAAAESAISLTRQVRETFWSAASTSSPALSYLSPRTQILYAFVREELGVKARRGDVFLGKQEVTIGSNVSKIYEAIKSGRINNVLLKMLA 716
               SCOP domains d1t6jb_ B: Phenylalanine ammonia-lyase, PAL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1t6jB01 B:39-271 Fumarase/aspartase (N-terminal domain)                                                                                                                                                                                  1t6jB02 B:272-545,B:649-716 Fumarase/aspartase (Central domain)                                                                                                                                                                                                                   -------------------------------------------------------------------------------------------------------1t6jB02 B:272-545,B:649-716 Fumarase/aspartase (Central domain)      CATH domains
           Pfam domains (1) ---------------------Lyase_aromatic-1t6jB01 B:60-565                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------Lyase_aromatic-1t6jB02 B:60-565                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhh.......eee.....hhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhh.-------------------.hhhhhhhhhh..........................hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..ee..........--hhhhhhhhhhhhh.....eeeeee..eeeeeehhhhhh.............hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhhhh...........----------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeehhhheee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhh..hhhhhhhhhhhhhhhhhhh..hhhhh..hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..................hhhhhhhhhhhhhhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------PAL_HISTIDASE    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1t6j B  39 TTQVTQVDIVEKmLAAPTDSTLELDGYSLNLGDVVSAARKGRPVRVKDSDEIRSKIDKSVEFLRSQ-------------------TEDAISLQKALLEHQLCGVLPSSFDSFRLGRGLENSLPLEVVRGAmTIRVNSLTRGHSAVRLVVLEALTNFLNHGITPIVPLRGTISa--DLSPLSYIAAAISGHPDSKVHVVHEGKEKILYAREAmALFNLEPVVLGPKEGLGLVNGTAVSASmATLALHDAHmLSLLSQSLTAmTVEAmVGHAGSFHPFLHDVTRPHPTQIEVAGNIRKLLEGSRFAVHHEEE----------RQDRYPLRTSPQWLGPLVSDLIHAHAVLTIEAGQSTTDNPLIDVENKTSHHGGNFQAAAVANTmEKTRLGLAQIGKLNFTQLTEmLNAGmNRGLPSCLAAEDPSLSYHCKGLDIAAAAYTSELGHLANPVTTHVQPAEmANQAVNSLALISARRTTESNDVLSLLLATHLYCVLQAIDLRAIEFEFKKQFGPAIVSLIDQHFGSAmTGSNLRDELVEKVNKTLAKRLEQTNSYDLVPRWHDAFSFAAGTVVEVLSSTSLSLAAVNAWKVAAAESAISLTRQVRETFWSAASTSSPALSYLSPRTQILYAFVREELGVKARRGDVFLGKQEVTIGSNVSKIYEAIKSGRINNVLLKmLA 716
                                    48  |     58        68        78        88        98     |   -         -     | 128       138       148       158       168|      178       188       198       208  |  | 218       228       238       248 |     258       268       278       288       298|    | 308       318       328       338       348         -|      368       378       388       398       408       418   |   428       438    |  448       458       468       478       488       498       508       518       528       538       548       558     | 568       578       588       598       608       618       628       638       648       658       668       678       688       698       708     |  
                                       51-MSE                                              104                 124                                          169-MSE                                   211-175                                250-MSE                     278-MSE   288-MSE    299-MSE|                                         348        359                                                            422-MSE              443-MSE|                                              497-MSE                                                            564-MSE                                                                                                                                               714-MSE
                                                                                                                                                                                                         214                                                                                       304-MSE                                                                                                                                         448-MSE

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)

Fungus (Rhodosporidium toruloides) [TaxId: 5286] (3)

1a	d1t6ja_	A:
1b	d1t6jb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Fumarase C; Chain B, domain 1 (57)

Homologous Superfamily: Fumarase/aspartase (N-terminal domain) (57)

Rhodosporidium toruloides. Organism_taxid: 5286. (2)

1a	1t6jA01	A:39-271
1b	1t6jB01	B:39-271

Architecture: Up-down Bundle (3216)

Topology: Fumarase C; Chain A, domain 2 (60)

Homologous Superfamily: Fumarase/aspartase (Central domain) (59)

Rhodosporidium toruloides. Organism_taxid: 5286. (2)

2a	1t6jA02	A:272-545,A:649-716
2b	1t6jB02	B:272-545,B:649-716

Asymmetric Unit(hide GO term definitions)

Chain A,B (PALY_RHOTO | P11544)

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.
	GO:0052883	tyrosine ammonia-lyase activity	Catalysis of the reaction: L-tyrosine = NH(4)(+) + trans-4-coumarate.
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.

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	PALY_RHOTO \| P11544	:	1t6p 1y2m

1t6p	PHENYLALANINE AMMONIA LYASE MONOCLONAL PHASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 29)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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