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(-) Description

Title :  CRYSTAL STRUCTURE OF A TAXUS PHENYLALANINE AMINOMUTASE
 
Authors :  L. Feng, J. H. Geiger
Date :  16 Jul 10  (Deposition) - 23 Mar 11  (Release) - 20 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.38
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Aminomutase, Taxol Biosynthetic Pathway, Mio, Phenylalanine, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Feng, U. Wanninayake, S. Strom, J. Geiger, K. D. Walker
Mechanistic, Mutational, And Structural Evaluation Of A Taxus Phenylalanine Aminomutase.
Biochemistry V. 50 2919 2011
PubMed-ID: 21361343  |  Reference-DOI: 10.1021/BI102067R

(-) Compounds

Molecule 1 - PHENYLALANINE AMMONIA-LYASE
    Chains: A, B
    EC Number: 4.3.1.24
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: CANADA YEW, GROUND-HEMLOCK
    Organism Scientific: TAXUS CANADENSIS
    Organism Taxid: 88032

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1MDO2Mod. Amino Acid{2-[(1S)-1-AMINOETHYL]-5-HYDROXY-4-METHYL-1H-IMIDAZOL-1-YL}ACETIC ACID
2TCA2Ligand/IonPHENYLETHYLENECARBOXYLIC ACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1MDO2Mod. Amino Acid{2-[(1S)-1-AMINOETHYL]-5-HYDROXY-4-METHYL-1H-IMIDAZOL-1-YL}ACETIC ACID
2TCA2Ligand/IonPHENYLETHYLENECARBOXYLIC ACID
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1MDO4Mod. Amino Acid{2-[(1S)-1-AMINOETHYL]-5-HYDROXY-4-METHYL-1H-IMIDAZOL-1-YL}ACETIC ACID
2TCA4Ligand/IonPHENYLETHYLENECARBOXYLIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:319 , ARG A:325 , TYR B:80 , LEU B:104 , MDO B:176 , ASN B:355 , PHE B:371 , GLU B:455BINDING SITE FOR RESIDUE TCA B 699
2AC2SOFTWARETYR A:80 , GLY A:87 , LEU A:104 , MDO A:176 , PHE A:371 , GLN B:319 , ARG B:325BINDING SITE FOR RESIDUE TCA A 699

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NZ4)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:76 -Ala A:77
2Asn A:355 -Pro A:356
3Asn B:355 -Pro B:356

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NZ4)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PAL_HISTIDASEPS00488 Phenylalanine and histidine ammonia-lyases signature.PAM_TAXCA171-187
 		  2A:171-187
B:171-187
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PAL_HISTIDASEPS00488 Phenylalanine and histidine ammonia-lyases signature.PAM_TAXCA171-187
 		  2A:171-187
B:171-187
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PAL_HISTIDASEPS00488 Phenylalanine and histidine ammonia-lyases signature.PAM_TAXCA171-187
 		  4A:171-187
B:171-187

(-) Exons   (0, 0)

(no "Exon" information available for 3NZ4)

(-) 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:654
 aligned with PAM_TAXCA | Q6GZ04 from UniProtKB/Swiss-Prot  Length:698

    Alignment length:672
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676  
            PAM_TAXCA     7 SRSHVKDILGLINTFNEVKKITVDGTTPITVAHVAALARRHDVKVALEAEQCRARVETCSSWVQRKAEDGADIYGVTTGFGACSSRRTNQLSELQESLIRCLLAGVFTKGCASSVDELPATATRSAMLLRLNSFTYGCSGIRWEVMEALEKLLNSNVSPKVPLRGSVSASGDLIPLAYIAGLLIGKPSVVARIGDDVEVPAPEALSRVGLRPFKLQAKEGLALVNGTSFATALASTVMYDANVLLLLVETLCGMFCEVIFGREEFAHPLIHKVKPHPGQIESAELLEWLLRSSPFQDLSREYYSIDKLKKPKQDRYALRSSPQWLAPLVQTIRDATTTVETEVNSANDNPIIDHANDRALHGANFQGSAVGFYMDYVRIAVAGLGKLLFAQFTELMIEYYSNGLPGNLSLGPDLSVDYGLKGLDIAMAAYSSELQYLANPVTTHVHSAEQHNQDINSLALISARKTEEALDILKLMIASHLTAMCQAVDLRQLEEALVKVVENVVSTLADECGLPNDTKARLLYVAKAVPVYTYLESPCDPTLPLLLGLEQSCFGSILALHKKDGIETDTLVDRLAEFEKRLSDRLENEMTAVRVLYEKKGHKTADNNDALVRIQGSRFLPFYRFVREELDTGVMSARREQTPQEDVQKVFDAIADGRITVPLLHCLQGFLG 678
               SCOP domains d3nz4a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.eeee......hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhh..........hhhhh.....hhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.eee.........-.-hhhhhhhhhhhhh.....eeee....eeehhhhhhhh.........hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeehhhheee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...hhhhh..hhhhhhhhhhhhhhhhhhh..hhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh..----hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.------------.hhhhh.hhhhhhhhhh.............hhhhhhhhhhhhhhhh.hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------PAL_HISTIDASE    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nz4 A   7 SRSHVKDILGLINTFNEVKKITVDGTTPITVAHVAALARRHDVKVALEAEQCRARVETCSSWVQRKAEDGADIYGVTTGFGACSSRRTNQLSELQESLIRCLLAGVFTKGCASSVDELPATVTRSAMLLRLNSFTYGCSGIRWEVMEALEKLLNSNVSPKVPLRGSVS-a-DLIPLAYIAGLLIGKPSVIARIGDDVEVPAPEALSRVGLRPFKLQAKEGLALVNGTSFATALASTVMYDANVLLLLVETLCGMFCEVIFGREEFAHPLIHKVKPHPGQIESAELLEWLLRSSPFQDLSREYYSIDKLKKPKQDRYALRSSPQWLAPLVQTIRDATTTVETEVNSANDNPIIDHANDRALHGANFQGSAVGFYMDYVRIAVAGLGKLLFAQFTELMIEYYSNGLPGNLSLGPDLSVDYGLKGLDIAMAAYSSELQYLANPVTTHVHSAEQHNQDINSLALISARKTDEALDILKLMIASHLTAMCQAVDLRQLEEALVKVVENVVSTLADECGLPNDTKARLLYVAKAVPVYTYLESPCDPTLPLLLGLKQSCFGSILALHK----ETDTLVDRLAEFEKRLSDRLENEMTAVRVLYEK------------VRIQGSRFLPFYRFVRDELDTGVMSARREQTPQEDVQKVFDAIADGRITVPLLHCLQGFLG 678
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176 |     186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566 |    |576       586       596        |-         - |     626       636       646       656       666       676  
                                                                                                                                                                                                 174 | |                                                                                                                                                                                                                                                                                                                                                                                                   568  573                             605          618                                                            
                                                                                                                                                                                                   176-MDO                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
                                                                                                                                                                                                     178                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:656
 aligned with PAM_TAXCA | Q6GZ04 from UniProtKB/Swiss-Prot  Length:698

    Alignment length:672
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676  
            PAM_TAXCA     7 SRSHVKDILGLINTFNEVKKITVDGTTPITVAHVAALARRHDVKVALEAEQCRARVETCSSWVQRKAEDGADIYGVTTGFGACSSRRTNQLSELQESLIRCLLAGVFTKGCASSVDELPATATRSAMLLRLNSFTYGCSGIRWEVMEALEKLLNSNVSPKVPLRGSVSASGDLIPLAYIAGLLIGKPSVVARIGDDVEVPAPEALSRVGLRPFKLQAKEGLALVNGTSFATALASTVMYDANVLLLLVETLCGMFCEVIFGREEFAHPLIHKVKPHPGQIESAELLEWLLRSSPFQDLSREYYSIDKLKKPKQDRYALRSSPQWLAPLVQTIRDATTTVETEVNSANDNPIIDHANDRALHGANFQGSAVGFYMDYVRIAVAGLGKLLFAQFTELMIEYYSNGLPGNLSLGPDLSVDYGLKGLDIAMAAYSSELQYLANPVTTHVHSAEQHNQDINSLALISARKTEEALDILKLMIASHLTAMCQAVDLRQLEEALVKVVENVVSTLADECGLPNDTKARLLYVAKAVPVYTYLESPCDPTLPLLLGLEQSCFGSILALHKKDGIETDTLVDRLAEFEKRLSDRLENEMTAVRVLYEKKGHKTADNNDALVRIQGSRFLPFYRFVREELDTGVMSARREQTPQEDVQKVFDAIADGRITVPLLHCLQGFLG 678
               SCOP domains d3nz4b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.eeee......hhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhh...........hhhhh.....hhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhheee.........-.-hhhhhhhhhhhhh.....eeee....eeehhhhhhh..........hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeehhhheee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh..........hhhhhhhhhhhhhhhhhhh..hhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...--.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.------------hhhhhh.hhhhhhhhhh.............hhhhhhhhhhhhhhhh.hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------PAL_HISTIDASE    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nz4 B   7 SRSHVKDILGLINTFNEVKKITVDGTTPITVAHVAALARRHDVKVALEAEQCRARVETCSSWVQRKAEDGADIYGVTTGFGACSSRRTNQLSELQESLIRCLLAGVFTKGCASSVDELPATVTRSAMLLRLNSFTYGCSGIRWEVMEALEKLLNSNVSPKVPLRGSVS-a-DLIPLAYIAGLLIGKPSVIARIGDDVEVPAPEALSRVGLRPFKLQAKEGLALVNGTSFATALASTVMYDANVLLLLVETLCGMFCEVIFGREEFAHPLIHKVKPHPGQIESAELLEWLLRSSPFQDLSREYYSIDKLKKPKQDRYALRSSPQWLAPLVQTIRDATTTVETEVNSANDNPIIDHANDRALHGANFQGSAVGFYMDYVRIAVAGLGKLLFAQFTELMIEYYSNGLPGNLSLGPDLSVDYGLKGLDIAMAAYSSELQYLANPVTTHVHSAEQHNQDINSLALISARKTDEALDILKLMIASHLTAMCQAVDLRQLEEALVKVVENVVSTLADECGLPNDTKARLLYVAKAVPVYTYLESPCDPTLPLLLGLKQSCFGSILALHKK--IETDTLVDRLAEFEKRLSDRLENEMTAVRVLYEK------------VRIQGSRFLPFYRFVRDELDTGVMSARREQTPQEDVQKVFDAIADGRITVPLLHCLQGFLG 678
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176 |     186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566  |  | 576       586       596        |-         - |     626       636       646       656       666       676  
                                                                                                                                                                                                 174 | |                                                                                                                                                                                                                                                                                                                                                                                                    569  |                              605          618                                                            
                                                                                                                                                                                                   176-MDO                                                                                                                                                                                                                                                                                                                                                                                                     572                                                                                                          
                                                                                                                                                                                                     178
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NZ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3NZ4)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PAM_TAXCA | Q6GZ04)
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:0016869    intramolecular transferase activity, transferring amino groups    Catalysis of the transfer of an amino group from one position to another within a single molecule.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    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:0006558    L-phenylalanine metabolic process    The chemical reactions and pathways involving L-phenylalanine, the L-enantiomer of 2-amino-3-phenylpropanoic acid, i.e. (2S)-2-amino-3-phenylpropanoic acid.
    GO:0009821    alkaloid biosynthetic process    The chemical reactions and pathways resulting in the formation of alkaloids, nitrogen-containing natural products which are not otherwise classified as nonprotein amino acids, amines, peptides, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones, or primary metabolite (such as purine or pyrimidine bases).
    GO:0009820    alkaloid metabolic process    The chemical reactions and pathways involving alkaloids, nitrogen containing natural products which are not otherwise classified as peptides, nonprotein amino acids, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones or primary metabolites (such as purine or pyrimidine bases).
    GO:0009800    cinnamic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of cinnamic acid, 3-phenyl-2-propenoic acid.
    GO:0042617    paclitaxel biosynthetic process    The chemical reactions and pathways resulting in the formation of paclitaxel, an alkaloid compound used as an anticancer treatment.
    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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