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(-) Description

Title :  CRYSTAL STRUCTURE OF HOMO SAPIENS KYNURENINASE
 
Authors :  S. Lima, R. Khristoforov, C. Momany, R. S. Phillips
Date :  09 Aug 06  (Deposition) - 07 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Kynureninase, Kynurenine, Hydrolase, Hydroxykynurenine, Plp, Pyridoxal Phosphate, Quinolinic Acid, Hydroxyanthranilate, 3- Hydroxyanthranilate, Vitamin B6, Nad, Quinolinate (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Lima, R. Khristoforov, C. Momany, R. S. Phillips
Crystal Structure Of Homo Sapiens Kynureninase.
Biochemistry V. 46 2735 2007
PubMed-ID: 17300176  |  Reference-DOI: 10.1021/BI0616697

(-) Compounds

Molecule 1 - KYNURENINASE
    ChainsA
    EC Number3.7.1.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPCRT7OHKYN
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePCRT7/NT TOPO PET100
    GeneKYNU
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymL-KYNURENINE HYDROLASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CSX1Mod. Amino AcidS-OXY CYSTEINE
2PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CSX2Mod. Amino AcidS-OXY CYSTEINE
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:137 , THR A:138 , PHE A:165 , ASP A:168 , ASP A:250 , ALA A:252 , HIS A:253 , TYR A:275 , LYS A:276 , TRP A:305 , SER A:332 , ASN A:333 , HOH A:548BINDING SITE FOR RESIDUE PLP A 544

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn A:429 -Pro A:430

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049724R188QKYNU_HUMANPolymorphism2304705AR188Q
2UniProtVAR_054401T198AKYNU_HUMANDisease (HYXKY)606231307AT198A
3UniProtVAR_022092K412EKYNU_HUMANPolymorphism9013AK412E

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049724R188QKYNU_HUMANPolymorphism2304705AR188Q
2UniProtVAR_054401T198AKYNU_HUMANDisease (HYXKY)606231307AT198A
3UniProtVAR_022092K412EKYNU_HUMANPolymorphism9013AK412E

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2HZP)

(-) Exons   (13, 13)

Asymmetric Unit (13, 13)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002641701aENSE00001468361chr2:143635067-143635305239KYNU_HUMAN-00--
1.4ENST000002641704ENSE00001273432chr2:143642918-143643105188KYNU_HUMAN1-57571A:6-5752
1.5aENST000002641705aENSE00000964247chr2:143676178-143676298121KYNU_HUMAN57-97411A:57-9741
1.6ENST000002641706ENSE00001636901chr2:143685228-14368531083KYNU_HUMAN97-125291A:97-12529
1.9ENST000002641709ENSE00001617905chr2:143712379-14371244062KYNU_HUMAN125-145211A:125-14521
1.10ENST0000026417010ENSE00000964250chr2:143713772-14371384372KYNU_HUMAN146-169241A:146-16924
1.11aENST0000026417011aENSE00000964251chr2:143715210-14371528475KYNU_HUMAN170-194251A:170-19425
1.12ENST0000026417012ENSE00000964252chr2:143718193-143718339147KYNU_HUMAN195-243491A:195-24349
1.13ENST0000026417013ENSE00000964253chr2:143742653-14374275199KYNU_HUMAN244-276331A:244-27633
1.14ENST0000026417014ENSE00000964254chr2:143743517-14374359074KYNU_HUMAN277-301251A:277-30125
1.17ENST0000026417017ENSE00000964255chr2:143787196-14378724853KYNU_HUMAN301-319191A:301-31919
1.18ENST0000026417018ENSE00000964256chr2:143790805-14379089086KYNU_HUMAN319-347291A:319-34729
1.19ENST0000026417019ENSE00000777481chr2:143797997-143798227231KYNU_HUMAN348-424771A:348-424 (gaps)77
1.20bENST0000026417020bENSE00001158917chr2:143799616-143799890275KYNU_HUMAN425-465411A:425-46036

(-) 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:447
 aligned with KYNU_HUMAN | Q16719 from UniProtKB/Swiss-Prot  Length:465

    Alignment length:455
                                    15        25        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     
           KYNU_HUMAN     6 LELPADTVQRIAAELKCHPTDERVALHLDEEDKLRHFRECFYIPKIQDLPPVDLSLVNKDENAIYFLGNSLGLQPKMVKTYLEEELDKWAKIAAYGHEVGKRPWITGDESIVGLMKDIVGANEKEIALMNALTVNLHLLMLSFFKPTPKRYKILLEAKAFPSDHYAIESQLQLHGLNIEESMRMIKPREGEETLRIEDILEVIEKEGDSIAVILFSGVHFYTGQHFNIPAITKAGQAKGCYVGFDLAHAVGNVELYLHDWGVDFACWCSYKYLNAGAGGIAGAFIHEKHAHTIKPALVGWFGHELSTRFKMDNKLQLIPGVCGFRISNPPILLVCSLHASLEIFKQATMKALRKKSVLLTGYLEYLIKHNYGKDKAATKKPVVNIITPSHVEERGCQLTITFSVPNKDVFQELEKRGVVCDKRNPNGIRVAPVPLYNSFHDVYKFTNLLTSILDS 460
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhh.ee..hhhhh..............ee........ee.hhhhhhhhhhhhhhhhhhhhhh....hhhhh...hhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhh..hhhhheeee.........hhhhhhhhhhhhh..eeeeeee..........hhhhhhhhhhhh..eeeee..........hhhhhh..eeee..............eeee.hhhh........hhhhhhhhhhh..........hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..--------.eee....hhhhh...eeeee.....hhhhhhhh..ee.eee...eeee.......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q---------A---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------E------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4  PDB: A:6-57 UniProt: 1-57 [INCOMPLETE]    ---------------------------------------Exon 1.6  PDB: A:97-125      --------------------Exon 1.10  PDB: A:146-16Exon 1.11a  PDB: A:170-19Exon 1.12  PDB: A:195-243 UniProt: 195-243       Exon 1.13  PDB: A:244-276        Exon 1.14  PDB: A:277-301-----------------Exon 1.18  PDB: A:319-347    Exon 1.19  PDB: A:348-424 (gaps) UniProt: 348-424                            Exon 1.20b  PDB: A:425-460           Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------Exon 1.5a  PDB: A:57-97 UniProt: 57-97   ---------------------------Exon 1.9             -----------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.17          --------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2hzp A   6 LELPADTVQRIAAELKCHPTDERVALHLDEEDKLRHFREcFYIPKIQDLPPVDLSLVNKDENAIYFLGNSLGLQPKMVKTYLEEELDKWAKIAAYGHEVGKRPWITGDESIVGLMKDIVGANEKEIALMNALTVNLHLLMLSFFKPTPKRYKILLEAKAFPSDHYAIESQLQLHGLNIEESMRMIKPREGEETLRIEDILEVIEKEGDSIAVILFSGVHFYTGQHFNIPAITKAGQAKGCYVGFDLAHAVGNVELYLHDWGVDFACWCSYKYLNAGAGGIAGAFIHEKHAHTIKPALVGWFGHELSTRFKMDNKLQLIPGVCGFRISNPPILLVCSLHASLEIFKQATMKALRKKSVLLTGYLEYLIKHNYGK--------VVNIITPSHVEERGCQLTITFSVPNKDVFQELEKRGVVCDKRNPNGIRVAPVPLYNSFHDVYKFTNLLTSILDS 460
                                    15        25        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  |      - |     395       405       415       425       435       445       455     
                                                                  45-CSX                                                                                                                                                                                                                                                                                                                                      378      387                                                                         

   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)
Chain A   (KYNU_HUMAN | Q16719)
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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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:0034341    response to interferon-gamma    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-gamma stimulus. Interferon-gamma is also known as type II interferon.
    GO:0034516    response to vitamin B6    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vitamin B6 stimulus. Vitamin B6 encompasses pyridoxal, pyridoxamine and pyridoxine and the active form, pyridoxal phosphate.
    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.
    GO:0019442    tryptophan catabolic process to acetyl-CoA    The chemical reactions and pathways resulting in the breakdown of tryptophan into other compounds, including acetyl-CoA.
    GO:0019441    tryptophan catabolic process to kynurenine    The chemical reactions and pathways resulting in the breakdown of tryptophan into other compounds, including kynurenine.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KYNU_HUMAN | Q167193e9k

(-) Related Entries Specified in the PDB File

1qz9 PSEUDOMONAS FLUORESCENS KYNURENINASE