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(-) Description

Title :  CRYSTAL STRUCTURE OF PHENYLALANINE AMMONIA-LYASE FROM NOSTOC PUNCTIFORME
 
Authors :  G. V. Louie, M. C. Moffitt, M. E. Bowman, J. Pence, J. P. Noel, B. S. Moore
Date :  20 Nov 06  (Deposition) - 06 Feb 07  (Release) - 09 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Methylidene Imidazolone Prosthetic Group (Autocatalytically Formed By Internal Tripeptide Segment Ala167-Ser168-Gly169), Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Moffitt, G. V. Louie, M. E. Bowman, J. Pence, J. P. Noel, B. S. Moore
Discovery Of Two Cyanobacterial Phenylalanine Ammonia Lyases: Kinetic And Structural Characterization.
Biochemistry V. 46 1004 2007
PubMed-ID: 17240984  |  Reference-DOI: 10.1021/BI061774G

(-) Compounds

Molecule 1 - NOSTOC PUNCTIFORME PHENYLALANINE AMMONIA LYASE
    Chains: A
    EC Number: 4.3.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PHIS8
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: NOSTOC PUNCTIFORME
    Organism Taxid: 63737
    Strain: PCC 73102

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1MDO1Mod. Amino Acid{2-[(1S)-1-AMINOETHYL]-4-METHYLIDENE-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MDO4Mod. Amino Acid{2-[(1S)-1-AMINOETHYL]-4-METHYLIDENE-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 2NYF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn A:347 -Pro A:348

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PAL_HISTIDASEPS00488 Phenylalanine and histidine ammonia-lyases signature.PAL_NOSP7163-179  1A:163-179
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PAL_HISTIDASEPS00488 Phenylalanine and histidine ammonia-lyases signature.PAL_NOSP7163-179  4A:163-179

(-) Exons   (0, 0)

(no "Exon" information available for 2NYF)

(-) Sequences/Alignments

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:511
 aligned with PAL_NOSP7 | B2J528 from UniProtKB/Swiss-Prot  Length:569

    Alignment length:543
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563   
            PAL_NOSP7    24 SIVTVGDRNLTIDEVVNVARHGTQVRLTDNADVIRGVQASCDYINNAVETAQPIYGVTSGFGGMADVVISREQAAELQTNLIWFLKSGAGNKLSLADVRAAMLLRANSHLYGASGIRLELIQRIETFLNAGVTPHVYEFGSIGASGDLVPLSYITGALIGLDPSFTVDFDGKEMDAVTALSRLGLPKLQLQPKEGLAMMNGTSVMTGIAANCVYDAKVLLALTMGVHALAIQGLYGTNQSFHPFIHQCKPHPGQLWTADQMFSLLKDSSLVREELDGKHEYRGKDLIQDRYSLRCLAQFIGPIVDGVSEITKQIEVEMNSVTDNPLIDVENQVSYHGGNFLGQYVGVTMDRLRYYIGLLAKHIDVQIALLVSPEFSNGLPPSLVGNSDRKVNMGLKGLQISGNSIMPLLSFYGNSLADRFPTHAEQFNQNINSQGYISANLTRRSVDIFQNYMAIALMFGVQAVDLRTYKMKGHYDARTCLSPNTVQLYTAVCEVVGKPLTSVRPYIWNDNEQCLDEHIARISADIAGGGLIVQAVEHIFSSL 566
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhhhhh-----------------.hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhheee..eee.....--hhhhhhhhhhhhh......eeee..eeeehhhhhhhh.........hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhhhh.........-------------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeehhhheee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh..........hhhhhhhhhhhhhhhhhhh..hhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------PAL_HISTIDASE    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nyf A  24 SIVTVGDRNLTIDEVVNVARHGTQVRLTDNADVIRGVQASCDYINNAVETA-----------------ISREQAAELQTNLIWFLKSGAGNKLSLADVRAAMLLRANSHLYGASGIRLELIQRIETFLNAGVTPHVYEFGSIGa--DLVPLSYITGALIGLDPSFTVDFDGKEMDAVTALSRLGLPKLQLQPKEGLAMMNGTSVMTGIAANCVYDAKVLLALTMGVHALAIQGLYGTNQSFHPFIHQCKPHPGQLWTADQMFSLLKDSSLVREE-------------QDRYSLRCLAQFIGPIVDGVSEITKQIEVEMNSVTDNPLIDVENQVSYHGGNFLGQYVGVTMDRLRYYIGLLAKHIDVQIALLVSPEFSNGLPPSLVGNSDRKVNMGLKGLQISGNSIMPLLSFYGNSLADRFPTHAEQFNQNINSQGYISANLTRRSVDIFQNYMAIALMFGVQAVDLRTYKMKGHYDARTCLSPNTVQLYTAVCEVVGKPLTSVRPYIWNDNEQCLDEHIARISADIAGGGLIVQAVEHIFSSL 566
                                    33        43        53        63        73|        -        93       103       113       123       133       143       153       163   |  |173       183       193       203       213       223       233       243       253       263       273       283       293   |     -       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563   
                                                                             74                92                                                                        167-MDO                                                                                                                           297           311                                                                                                                                                                                                                                                               
                                                                                                                                                                            170
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2NYF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (PAL_NOSP7 | B2J528)
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:0009072    aromatic amino acid family metabolic process    The chemical reactions and pathways involving aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
    GO:0009800    cinnamic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of cinnamic acid, 3-phenyl-2-propenoic acid.
    GO:0009699    phenylpropanoid biosynthetic process    The chemical reactions and pathways resulting in the formation of aromatic derivatives of trans-cinnamic acid.
    GO:0009698    phenylpropanoid metabolic process    The chemical reactions and pathways involving aromatic derivatives of trans-cinnamic acid.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
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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 Related Entries

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(-) Related Entries Specified in the PDB File

1gkm HISTIDINE AMMONIA-LYASE FROM PSEUDOMONAS PUTIDA
1t6j PHENYLALANINE AMMONIA-LYASE FROM YEAST
1w27 PHENYLALANINE AMMONIA-LYASE FROM PARSLEY
1y2m PHENYLALANINE AMMONIA-LYASE FROM YEAST