Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF PHENYLALANINE AMMONIA-LYASE FROM YEAST RHODODPORIDIUM TORULOIDES
 
Authors :  L. Wang, A. Gamez, C. N. Sarkissian, M. Straub, M. G. Patch, G. W. Han, C. R R. C. Stevens
Date :  22 Nov 04  (Deposition) - 01 Nov 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Alpha Helices, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Wang, A. Gamez, C. N. Sarkissian, M. Straub, M. G. Patch, G. W. Han, S. Striepeke, P. Fitzpatrick, C. R. Scriver, R. C. Stevens
Structure-Based Chemical Modification Strategy For Enzyme Replacement Treatment Of Phenylketonuria.
Mol. Genet. Metab. V. 86 134 2005
PubMed-ID: 16006165  |  Reference-DOI: 10.1016/J.YMGME.2005.05.012
(for further references see the PDB file header)

(-) Compounds

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

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 53)

Asymmetric/Biological Unit (1, 53)
No.NameCountTypeFull Name
1MSE53Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1Y2M)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y2M)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:397 -Pro A:398
2Asn B:397 -Pro B:398
3Asn C:397 -Pro C:398
4Asn D:397 -Pro D:398

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y2M)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PAL_HISTIDASEPS00488 Phenylalanine and histidine ammonia-lyases signature.PALY_RHOTO207-223
 
 
 		  4A:207-223
B:207-223
C:207-223
D:207-223

(-) Exons   (0, 0)

(no "Exon" information available for 1Y2M)

(-) Sequences/Alignments

Asymmetric/Biological 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:665
 aligned with PALY_RHOTO | P11544 from UniProtKB/Swiss-Prot  Length:716

    Alignment length:690
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715
           PALY_RHOTO    26 ASTNLAVAGSHLPTTQVTQVDIVEKMLAAPTDSTLELDGYSLNLGDVVSAARKGRPVRVKDSDEIRSKIDKSVEFLRSQLSMSVYGVTTGFGGSADTRTEDAISLQKALLEHQLCGVLPSSFDSFRLGRGLENSLPLEVVRGAMTIRVNSLTRGHSAVRLVVLEALTNFLNHGITPIVPLRGTISASGDLSPLSYIAAAISGHPDSKVHVVHEGKEKILYAREAMALFNLEPVVLGPKEGLGLVNGTAVSASMATLALHDAHMLSLLSQSLTAMTVEAMVGHAGSFHPFLHDVTRPHPTQIEVAGNIRKLLEGSRFAVHHEEEVKVKDDEGILRQDRYPLRTSPQWLGPLVSDLIHAHAVLTIEAGQSTTDNPLIDVENKTSHHGGNFQAAAVANTMEKTRLGLAQIGKLNFTQLTEMLNAGMNRGLPSCLAAEDPSLSYHCKGLDIAAAAYTSELGHLANPVTTHVQPAEMANQAVNSLALISARRTTESNDVLSLLLATHLYCVLQAIDLRAIEFEFKKQFGPAIVSLIDQHFGSAMTGSNLRDELVEKVNKTLAKRLEQTNSYDLVPRWHDAFSFAAGTVVEVLSSTSLSLAAVNAWKVAAAESAISLTRQVRETFWSAASTSSPALSYLSPRTQILYAFVREELGVKARRGDVFLGKQEVTIGSNVSKIYEAIKSGRINNVLLKML 715
               SCOP domains d1y2ma_ A: Phenylalanine ammonia-lyase, PAL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1y2mA01 A:26-271 Fumarase/aspartase (N-terminal domain)                                                                                                                                                                                               1y2mA02 A:272-545,A:649-715 Fumarase/aspartase (Central domain)                                                                                                                                                                                                                   -------------------------------------------------------------------------------------------------------1y2mA02 A:272-545,A:649-715 Fumarase/aspartase (Central domain)     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhh........hhhhhhhhhhh......eee.....hhhhhhhhhhh...eee..hhhhhhhhhhhhhhhh---------------------hhhhhhhhhhhhhhhh......hhhhh..........hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..ee............hhhhhhhhhhhhh.....eeeeee..eeeeeehhhhhhhh.........hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhhhh......hhhhhh----........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eee....eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh..hhhhh..hhhhhhhhhhhhhhhhhhh..hhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh........hhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PAL_HISTIDASE    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1y2m A  26 ASTNLAVAGSHLPTTQVTQVDIVEKmLAAPTDSTLELDGYSLNLGDVVSAARKGRPVRVKDSDEIRSKIDKSVEFLR---------------------TEDAISLQKALLEHQLCGVLPSSFDSFRLGRGLENSLPLEVVRGAmTIRVNSLTRGHSAVRLVVLEALTNFLNHGITPIVPLRGTISASGDLSPLSYIAAAISGHPDSKVHVVHEGKEKILYAREAmALFNLEPVVLGPKEGLGLVNGTAVSASmATLALHDAHmLSLLSQSLTAmTVEAmVGHAGSFHPFLHDVTRPHPTQIEVAGNIRKLLEGSRFAVHHEEEV----DEGILRQDRYPLRTSPQWLGPLVSDLIHAHAVLTIEAGQSTTDNPLIDVENKTSHHGGNFQAAAVANTmEKTRLGLAQIGKLNFTQLTEmLNAGmNRGLPSCLAAEDPSLSYHCKGLDIAAAAYTSELGHLANPVTTHVQPAEmANQAVNSLALISARRTTESNDVLSLLLATHLYCVLQAIDLRAIEFEFKKQFGPAIVSLIDQHFGSAmTGSNLRDELVEKVNKTLAKRLEQTNSYDLVPRWHDAFSFAAGTVVEVLSSTSLSLAAVNAWKVAAAESAISLTRQVRETFWSAASTSSPALSYLSPRTQILYAFVREELGVKARRGDVFLGKQEVTIGSNVSKIYEAIKSGRINNVLLKmL 715
                                    35        45     |  55        65        75        85        95      |  -         -       125       135       145       155       165   |   175       185       195       205       215       225       235       245    |  255       265       275  |    285  |    295   |   305       315       325       335       345   |   355       365       375       385       395       405       415      |425       435       445  |    455       465       475       485       495 |     505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715
                                                    51-MSE                                            102                   124                                          169-MSE                                                                          250-MSE                     278-MSE   288-MSE    299-MSE|                                          349  354                                                                 422-MSE              443-MSE|                                              497-MSE                                                            564-MSE                                                                                                                                               714-MSE
                                                                                                                                                                                                                                                                                                                304-MSE                                                                                                                                         448-MSE                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:669
 aligned with PALY_RHOTO | P11544 from UniProtKB/Swiss-Prot  Length:716

    Alignment length:691
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715 
           PALY_RHOTO    26 ASTNLAVAGSHLPTTQVTQVDIVEKMLAAPTDSTLELDGYSLNLGDVVSAARKGRPVRVKDSDEIRSKIDKSVEFLRSQLSMSVYGVTTGFGGSADTRTEDAISLQKALLEHQLCGVLPSSFDSFRLGRGLENSLPLEVVRGAMTIRVNSLTRGHSAVRLVVLEALTNFLNHGITPIVPLRGTISASGDLSPLSYIAAAISGHPDSKVHVVHEGKEKILYAREAMALFNLEPVVLGPKEGLGLVNGTAVSASMATLALHDAHMLSLLSQSLTAMTVEAMVGHAGSFHPFLHDVTRPHPTQIEVAGNIRKLLEGSRFAVHHEEEVKVKDDEGILRQDRYPLRTSPQWLGPLVSDLIHAHAVLTIEAGQSTTDNPLIDVENKTSHHGGNFQAAAVANTMEKTRLGLAQIGKLNFTQLTEMLNAGMNRGLPSCLAAEDPSLSYHCKGLDIAAAAYTSELGHLANPVTTHVQPAEMANQAVNSLALISARRTTESNDVLSLLLATHLYCVLQAIDLRAIEFEFKKQFGPAIVSLIDQHFGSAMTGSNLRDELVEKVNKTLAKRLEQTNSYDLVPRWHDAFSFAAGTVVEVLSSTSLSLAAVNAWKVAAAESAISLTRQVRETFWSAASTSSPALSYLSPRTQILYAFVREELGVKARRGDVFLGKQEVTIGSNVSKIYEAIKSGRINNVLLKMLA 716
               SCOP domains d1y2mb_ B    : Phenylalanine ammonia-lyase, PAL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1y2mB01 B    :26-271 Fumarase/aspartase (N-terminal domain)                                                                                                                                                                                           1y2mB02 B:272-545,B:649-716 Fumarase/aspartase (Central domain)                                                                                                                                                                                                                   -------------------------------------------------------------------------------------------------------1y2mB02 B:272-545,B:649-716 Fumarase/aspartase (Central domain)      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh----....hhhhhhhhhhh......eee.....hhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhhhhh---------------hhhhhhhhhhhhhhhh......hhhhh..........hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.ee............hhhhhhhhhhhhh.....eeeeee..eeeeeehhhhhhhh.........hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhhhh......hhhhhh.---........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eee....eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh..hhhhh..hhhhhhhhhhhhhhhhhhh..hhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh........hhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PAL_HISTIDASE    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y2m B  26 ASTNLAVAG----TTQVTQVDIVEKmLAAPTDSTLELDGYSLNLGDVVSAARKGRPVRVKDSDEIRSKIDKSVEFLRSQLSmS---------------TEDAISLQKALLEHQLCGVLPSSFDSFRLGRGLENSLPLEVVRGAmTIRVNSLTRGHSAVRLVVLEALTNFLNHGITPIVPLRGTISASGDLSPLSYIAAAISGHPDSKVHVVHEGKEKILYAREAmALFNLEPVVLGPKEGLGLVNGTAVSASmATLALHDAHmLSLLSQSLTAmTVEAmVGHAGSFHPFLHDVTRPHPTQIEVAGNIRKLLEGSRFAVHHEEEVK---DEGILRQDRYPLRTSPQWLGPLVSDLIHAHAVLTIEAGQSTTDNPLIDVENKTSHHGGNFQAAAVANTmEKTRLGLAQIGKLNFTQLTEmLNAGmNRGLPSCLAAEDPSLSYHCKGLDIAAAAYTSELGHLANPVTTHVQPAEmANQAVNSLALISARRTTESNDVLSLLLATHLYCVLQAIDLRAIEFEFKKQFGPAIVSLIDQHFGSAmTGSNLRDELVEKVNKTLAKRLEQTNSYDLVPRWHDAFSFAAGTVVEVLSSTSLSLAAVNAWKVAAAESAISLTRQVRETFWSAASTSSPALSYLSPRTQILYAFVREELGVKARRGDVFLGKQEVTIGSNVSKIYEAIKSGRINNVLLKmLA 716
                                    |-   |    45     |  55        65        75        85        95       105 ||      -       125       135       145       155       165   |   175       185       195       205       215       225       235       245    |  255       265       275  |    285  |    295   |   305       315       325       335       345    |  355       365       375       385       395       405       415      |425       435       445  |    455       465       475       485       495 |     505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715 
                                   34   39          51-MSE                                                 107-MSE          124                                          169-MSE                                                                          250-MSE                     278-MSE   288-MSE    299-MSE|                                           350 354                                                                 422-MSE              443-MSE|                                              497-MSE                                                            564-MSE                                                                                                                                               714-MSE
                                                                                                            108                                                                                                                                                                                                 304-MSE                                                                                                                                         448-MSE                                                                                                                                                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:664
 aligned with PALY_RHOTO | P11544 from UniProtKB/Swiss-Prot  Length:716

    Alignment length:691
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715 
           PALY_RHOTO    26 ASTNLAVAGSHLPTTQVTQVDIVEKMLAAPTDSTLELDGYSLNLGDVVSAARKGRPVRVKDSDEIRSKIDKSVEFLRSQLSMSVYGVTTGFGGSADTRTEDAISLQKALLEHQLCGVLPSSFDSFRLGRGLENSLPLEVVRGAMTIRVNSLTRGHSAVRLVVLEALTNFLNHGITPIVPLRGTISASGDLSPLSYIAAAISGHPDSKVHVVHEGKEKILYAREAMALFNLEPVVLGPKEGLGLVNGTAVSASMATLALHDAHMLSLLSQSLTAMTVEAMVGHAGSFHPFLHDVTRPHPTQIEVAGNIRKLLEGSRFAVHHEEEVKVKDDEGILRQDRYPLRTSPQWLGPLVSDLIHAHAVLTIEAGQSTTDNPLIDVENKTSHHGGNFQAAAVANTMEKTRLGLAQIGKLNFTQLTEMLNAGMNRGLPSCLAAEDPSLSYHCKGLDIAAAAYTSELGHLANPVTTHVQPAEMANQAVNSLALISARRTTESNDVLSLLLATHLYCVLQAIDLRAIEFEFKKQFGPAIVSLIDQHFGSAMTGSNLRDELVEKVNKTLAKRLEQTNSYDLVPRWHDAFSFAAGTVVEVLSSTSLSLAAVNAWKVAAAESAISLTRQVRETFWSAASTSSPALSYLSPRTQILYAFVREELGVKARRGDVFLGKQEVTIGSNVSKIYEAIKSGRINNVLLKMLA 716
               SCOP domains d1y2mc_ C: Phenylalanine ammonia-lyase, PAL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1y2mC01 C:26-271 Fumarase/aspartase (N-terminal domain)                                                                                                                                                                                               1y2mC02 C:272-545,C:649-716 Fumarase/aspartase (Central domain)                                                                                                                                                                                                                   -------------------------------------------------------------------------------------------------------1y2mC02 C:272-545,C:649-716 Fumarase/aspartase (Central domain)      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh........hhhhhhhhhhh......eee.....hhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhh---------------------hhhhhhhhhhhhhhh......hhhhh..........hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.ee............hhhhhhhhhhhhh.....eeeeee..eeeeeehhhhhhhh.........hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhhhh..........------........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eee....eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh..hhhhh..hhhhhhhhhhhhhhhhhhh..hhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhh........hhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PAL_HISTIDASE    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y2m C  26 ASTNLAVAGSHLPTTQVTQVDIVEKmLAAPTDSTLELDGYSLNLGDVVSAARKGRPVRVKDSDEIRSKIDKSVEFLRS---------------------EDAISLQKALLEHQLCGVLPSSFDSFRLGRGLENSLPLEVVRGAmTIRVNSLTRGHSAVRLVVLEALTNFLNHGITPIVPLRGTISASGDLSPLSYIAAAISGHPDSKVHVVHEGKEKILYAREAmALFNLEPVVLGPKEGLGLVNGTAVSASmATLALHDAHmLSLLSQSLTAmTVEAmVGHAGSFHPFLHDVTRPHPTQIEVAGNIRKLLEGSRFAVHHEE------DEGILRQDRYPLRTSPQWLGPLVSDLIHAHAVLTIEAGQSTTDNPLIDVENKTSHHGGNFQAAAVANTmEKTRLGLAQIGKLNFTQLTEmLNAGmNRGLPSCLAAEDPSLSYHCKGLDIAAAAYTSELGHLANPVTTHVQPAEmANQAVNSLALISARRTTESNDVLSLLLATHLYCVLQAIDLRAIEFEFKKQFGPAIVSLIDQHFGSAmTGSNLRDELVEKVNKTLAKRLEQTNSYDLVPRWHDAFSFAAGTVVEVLSSTSLSLAAVNAWKVAAAESAISLTRQVRETFWSAASTSSPALSYLSPRTQILYAFVREELGVKARRGDVFLGKQEVTIGSNVSKIYEAIKSGRINNVLLKmLA 716
                                    35        45     |  55        65        75        85        95       | -         -       125       135       145       155       165   |   175       185       195       205       215       225       235       245    |  255       265       275  |    285  |    295   |   305       315       325       335       345 |     355       365       375       385       395       405       415      |425       435       445  |    455       465       475       485       495 |     505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715 
                                                    51-MSE                                             103                   125                                         169-MSE                                                                          250-MSE                     278-MSE   288-MSE    299-MSE|                                        347    354                                                                 422-MSE              443-MSE|                                              497-MSE                                                            564-MSE                                                                                                                                               714-MSE
                                                                                                                                                                                                                                                                                                                304-MSE                                                                                                                                         448-MSE                                                                                                                                                                                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:661
 aligned with PALY_RHOTO | P11544 from UniProtKB/Swiss-Prot  Length:716

    Alignment length:691
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715 
           PALY_RHOTO    26 ASTNLAVAGSHLPTTQVTQVDIVEKMLAAPTDSTLELDGYSLNLGDVVSAARKGRPVRVKDSDEIRSKIDKSVEFLRSQLSMSVYGVTTGFGGSADTRTEDAISLQKALLEHQLCGVLPSSFDSFRLGRGLENSLPLEVVRGAMTIRVNSLTRGHSAVRLVVLEALTNFLNHGITPIVPLRGTISASGDLSPLSYIAAAISGHPDSKVHVVHEGKEKILYAREAMALFNLEPVVLGPKEGLGLVNGTAVSASMATLALHDAHMLSLLSQSLTAMTVEAMVGHAGSFHPFLHDVTRPHPTQIEVAGNIRKLLEGSRFAVHHEEEVKVKDDEGILRQDRYPLRTSPQWLGPLVSDLIHAHAVLTIEAGQSTTDNPLIDVENKTSHHGGNFQAAAVANTMEKTRLGLAQIGKLNFTQLTEMLNAGMNRGLPSCLAAEDPSLSYHCKGLDIAAAAYTSELGHLANPVTTHVQPAEMANQAVNSLALISARRTTESNDVLSLLLATHLYCVLQAIDLRAIEFEFKKQFGPAIVSLIDQHFGSAMTGSNLRDELVEKVNKTLAKRLEQTNSYDLVPRWHDAFSFAAGTVVEVLSSTSLSLAAVNAWKVAAAESAISLTRQVRETFWSAASTSSPALSYLSPRTQILYAFVREELGVKARRGDVFLGKQEVTIGSNVSKIYEAIKSGRINNVLLKMLA 716
               SCOP domains d1y2md_       D: Phenylalanine ammonia-lyase, PAL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1y2mD01       D:26-271 Fumarase/aspartase (N-terminal domain)                                                                                                                                                                                         1y2mD02 D:272-545,D:649-716 Fumarase/aspartase (Central domain)                                                                                                                                                                                                                   -------------------------------------------------------------------------------------------------------1y2mD02 D:272-545,D:649-716 Fumarase/aspartase (Central domain)      CATH domains
           Pfam domains (1) -------      ---------------------Lyase_aromatic-1y2mD01 D:60-565                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------      ---------------------Lyase_aromatic-1y2mD02 D:60-565                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -------      ---------------------Lyase_aromatic-1y2mD03 D:60-565                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -------      ---------------------Lyase_aromatic-1y2mD04 D:60-565                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .......------....hhhhhhhhhhh......eee.....hhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhh--------------------hhhhhhhhhhhhhhhh......hhhhh..........hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..ee............hhhhhhhhhhhhh.....eeeeee..eeeeeehhhhhhhh.........hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhhhh......hhhhhh----........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eee....eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh..hhhhh..hhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhh........hhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PAL_HISTIDASE    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y2m D  26 ASTNLAV------TTQVTQVDIVEKmLAAPTDSTLELDGYSLNLGDVVSAARKGRPVRVKDSDEIRSKIDKSVEFLRS--------------------TEDAISLQKALLEHQLCGVLPSSFDSFRLGRGLENSLPLEVVRGAmTIRVNSLTRGHSAVRLVVLEALTNFLNHGITPIVPLRGTISASGDLSPLSYIAAAISGHPDSKVHVVHEGKEKILYAREAmALFNLEPVVLGPKEGLGLVNGTAVSASmATLALHDAHmLSLLSQSLTAmTVEAmVGHAGSFHPFLHDVTRPHPTQIEVAGNIRKLLEGSRFAVHHEEEV----DEGILRQDRYPLRTSPQWLGPLVSDLIHAHAVLTIEAGQSTTDNPLIDVENKTSHHGGNFQAAAVANTmEKTRLGLAQIGKLNFTQLTEmLNAGmNRGLPSCLAAEDPSLSYHCKGLDIAAAAYTSELGHLANPVTTHVQPAEmANQAVNSLALISARRTTESNDVLSLLLATHLYCVLQAIDLRAIEFEFKKQFGPAIVSLIDQHFGSAmTGSNLRDELVEKVNKTLAKRLEQTNSYDLVPRWHDAFSFAAGTVVEVLSSTSLSLAAVNAWKVAAAESAISLTRQVRETFWSAASTSSPALSYLSPRTQILYAFVREELGVKARRGDVFLGKQEVTIGSNVSKIYEAIKSGRINNVLLKmLA 716
                                  |  -   |    45     |  55        65        75        85        95       | -         -       125       135       145       155       165   |   175       185       195       205       215       225       235       245    |  255       265       275  |    285  |    295   |   305       315       325       335       345   |   355       365       375       385       395       405       415      |425       435       445  |    455       465       475       485       495 |     505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715 
                                 32     39          51-MSE                                             103                  124                                          169-MSE                                                                          250-MSE                     278-MSE   288-MSE    299-MSE|                                          349  354                                                                 422-MSE              443-MSE|                                              497-MSE                                                            564-MSE                                                                                                                                               714-MSE
                                                                                                                                                                                                                                                                                                                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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Lyase_aromatic] (3)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1y2m)
 
  Cis Peptide Bonds
    Asn A:397 - Pro A:398   [ RasMol ]  
    Asn B:397 - Pro B:398   [ RasMol ]  
    Asn C:397 - Pro C:398   [ RasMol ]  
    Asn D:397 - Pro D:398   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1y2m
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PALY_RHOTO | P11544
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  4.3.1.5
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PALY_RHOTO | P11544
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PALY_RHOTO | P11544: 1t6j 1t6p

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1Y2M)