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(-) Description

Title :  THE THREE DIMENSIONAL STRUCTURE OF KYNURENINASE FROM PSEUDOMONAS FLUORESCENS
 
Authors :  C. Momany, V. Levdikov, L. Blagova, S. Lima, R. S. Phillips
Date :  16 Sep 03  (Deposition) - 20 Jan 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Kynurenine, Tryptophan, Plp, Vitamin B6, Pyridoxal-5'-Phosphate, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Momany, V. Levdikov, L. Blagova, S. Lima, R. S. Phillips
Three-Dimensional Structure Of Kynureninase From Pseudomona Fluorescens.
Biochemistry V. 43 1193 2004
PubMed-ID: 14756555  |  Reference-DOI: 10.1021/BI035744E

(-) Compounds

Molecule 1 - KYNURENINASE
    ChainsA
    EC Number3.7.1.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPTZ18U
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism ScientificPSEUDOMONAS FLUORESCENS
    Organism Taxid294

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2P3G1Ligand/Ion3,6,9,12,15-PENTAOXAHEPTADECANE
3PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2P3G2Ligand/Ion3,6,9,12,15-PENTAOXAHEPTADECANE
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:204 , ARG A:375 , HOH A:1353BINDING SITE FOR RESIDUE CL A 601
2AC2SOFTWARETHR A:96 , THR A:97 , SER A:98 , PHE A:129 , THR A:131 , ASP A:132 , THR A:172 , ASP A:201 , ALA A:203 , HIS A:204 , CYS A:224 , TYR A:226 , LYS A:227 , TRP A:256 , GLY A:281 , THR A:282 , HOH A:1256BINDING SITE FOR RESIDUE PLP A 1227
3AC3SOFTWARETRP A:256 , HIS A:259 , ARG A:261 , MET A:265 , ARG A:369 , HOH A:1636BINDING SITE FOR RESIDUE P3G A 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QZ9)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gln A:144 -Gln A:145
2Gln A:145 -Gly A:146
3Glu A:370 -Pro A:371

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QZ9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1QZ9)

(-) Exons   (0, 0)

(no "Exon" information available for 1QZ9)

(-) 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:404
 aligned with KYNU_PSEFL | P83788 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:404
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401    
           KYNU_PSEFL     2 TTRNDCLALDAQDSLAPLRQQFALPEGVIYLDGNSLGARPVAALARAQAVIAEEWGNGLIRSWNSAGWRDLSERLGNRLATLIGARDGEVVVTDTTSINLFKVLSAALRVQATRSPERRVIVTETSNFPTDLYIAEGLADMLQQGYTLRLVDSPEELPQAIDQDTAVVMLTHVNYKTGYMHDMQALTALSHECGALAIWDLAHSAGAVPVDLHQAGADYAIGCTYKYLNGGPGSQAFVWVSPQLCDLVPQPLSGWFGHSRQFAMEPRYEPSNGIARYLCGTQPITSLAMVECGLDVFAQTDMASLRRKSLALTDLFIELVEQRCAAHELTLVTPREHAKRGSHVSFEHPEGYAVIQALIDRGVIGDYREPRIMRFGFTPLYTTFTEVWDAVQILGEILDRKTWA 405
               SCOP domains d1qz9a_ A: Kynureninase                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1qz9A01 A:2-40,A:302-405               ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1qz9A01 A:2-40,A:302-405 Aspartate Aminotransferase, domain 1                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh..hhhhhhhh......ee...........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh........eee..hhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhh...eeeeeee..........hhhhhhhhhhhhh.eeeee..........hhhhhh..eeee..............eeee.............hhhhh..............hhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....ee....hhhhh..eeeee..hhhhhhhhhhh..ee.eee...eeeee......hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qz9 A   2 TTRNDCLALDAQDSLAPLRQQFALPEGVIYLDGNSLGARPVAALARAQAVIAEEWGNGLIRSWNSAGWRDLSERLGNRLATLIGARDGEVVVTDTTSINLFKVLSAALRVQATRSPERRVIVTETSNFPTDLYIAEGLADMLQQGYTLRLVDSPEELPQAIDQDTAVVMLTHVNYKTGYMHDMQALTALSHECGALAIWDLAHSAGAVPVDLHQAGADYAIGCTYKYLNGGPGSQAFVWVSPQLCDLVPQPLSGWFGHSRQFAMEPRYEPSNGIARYLCGTQPITSLAMVECGLDVFAQTDMASLRRKSLALTDLFIELVEQRCAAHELTLVTPREHAKRGSHVSFEHPEGYAVIQALIDRGVIGDYREPRIMRFGFTPLYTTFTEVWDAVQILGEILDRKTWA 405
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401    

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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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1QZ9)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (KYNU_PSEFL | P83788)
molecular function
    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:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0030429    kynureninase activity    Catalysis of the reaction: L-kynurenine + H2O = anthranilate + L-alanine.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
biological process
    GO:0034354    'de novo' NAD biosynthetic process from tryptophan    The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD), beginning with the synthesis of tryptophan from simpler precursors; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
    GO:0097053    L-kynurenine catabolic process    The chemical reactions and pathways resulting in the breakdown of L-kynurenine, the L-enantiomer of the amino acid kynurenine (3-(2-aminobenzoyl)-alanine).
    GO:0009435    NAD biosynthetic process    The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide, a coenzyme present in most living cells and derived from the B vitamin nicotinic acid; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
    GO:0043420    anthranilate metabolic process    The chemical reactions and pathways involving anthranilate (2-aminobenzoate).
    GO:0019363    pyridine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base.
    GO:0019805    quinolinate biosynthetic process    The chemical reactions and pathways resulting in the formation of quinolinate, the anion of quinolinic acid, also known as 2,3-pyridinedicarboxylic acid.
    GO:0006569    tryptophan catabolic process    The chemical reactions and pathways resulting in the breakdown of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic 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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