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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN KYNURENINE AMINOTRANSFERASE I IN COMPLEX WITH L-PHE
 
Authors :  F. Rossi, Q. Han, J. Li, J. Li, M. Rizzi
Date :  06 Sep 04  (Deposition) - 08 Sep 04  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Kynurenine Pathway, Kynurenic Acid, Plp-Enzyme, Aminotransferase, Lyase, Multifunctional Enzyme, Pyridoxal Phosphate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Rossi, Q. Han, J. Li, J. Li, M. Rizzi
Crystal Structure Of Human Kynurenine Aminotransferase I
J. Biol. Chem. V. 279 50214 2004
PubMed-ID: 15364907  |  Reference-DOI: 10.1074/JBC.M409291200

(-) Compounds

Molecule 1 - KYNURENINE--OXOGLUTARATE TRANSAMINASE I
    ChainsA
    EC Number4.4.1.13
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    OrganLIVER
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymKYNURENINE AMINOTRANSFERASE I, KATI, GLUTAMINE-PHENYLPYRUVATE TRANSAMINASE, GLUTAMINE TRANSAMINASE K, GTK, CYSTEINE-S-CONJUGATE BETA-LYASE

 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
1PHE1Mod. Amino AcidPHENYLALANINE
2PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1PHE2Mod. Amino AcidPHENYLALANINE
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:63 , GLY A:99 , GLY A:100 , TYR A:101 , PHE A:125 , ASN A:181 , ASN A:185 , ASP A:213 , VAL A:215 , TYR A:216 , SER A:244 , LYS A:247 , LYS A:255 , PHE A:914 , HOH A:2148 , HOH A:2149BINDING SITE FOR RESIDUE PLP A1247
2AC2SOFTWARETRP A:18 , GLY A:36 , TYR A:63 , TYR A:101 , PHE A:125 , ASN A:185 , LYS A:247 , HIS A:279 , ARG A:398 , PLP A:1247 , HOH A:2013BINDING SITE FOR RESIDUE PHE A 914

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W7M)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Glu A:122 -Pro A:123
2Thr A:182 -Pro A:183
3Asn A:185 -Pro A:186

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W7M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1W7M)

(-) Exons   (12, 12)

Asymmetric Unit (12, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2cENST000003025862cENSE00001851283chr9:131644332-131644176157KAT1_HUMAN-00--
1.5bENST000003025865bENSE00002195023chr9:131607690-13160763259KAT1_HUMAN1-18181A:4-1815
1.6ENST000003025866ENSE00001143432chr9:131605080-131604933148KAT1_HUMAN18-67501A:18-6750
1.9bENST000003025869bENSE00002146235chr9:131600646-131600497150KAT1_HUMAN68-117501A:68-11750
1.10ENST0000030258610ENSE00001626071chr9:131600416-13160033087KAT1_HUMAN118-146291A:118-14629
1.11cENST0000030258611cENSE00001784290chr9:131600092-131599964129KAT1_HUMAN147-189431A:147-189 (gaps)43
1.12ENST0000030258612ENSE00001761291chr9:131599201-131599081121KAT1_HUMAN190-230411A:190-23041
1.13cENST0000030258613cENSE00001704435chr9:131598352-13159827677KAT1_HUMAN230-255261A:230-25526
1.14ENST0000030258614ENSE00001738063chr9:131598147-13159805890KAT1_HUMAN256-285301A:256-28530
1.15aENST0000030258615aENSE00001595628chr9:131597946-131597760187KAT1_HUMAN286-348631A:286-34863
1.16aENST0000030258616aENSE00001756602chr9:131597681-13159760280KAT1_HUMAN348-374271A:348-37427
1.17ENST0000030258617ENSE00001781922chr9:131596105-13159601987KAT1_HUMAN375-403291A:375-40329
1.18dENST0000030258618dENSE00001709974chr9:131595922-131595392531KAT1_HUMAN404-422191A:404-42118

(-) 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:416
 aligned with KAT1_HUMAN | Q16773 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:420
                                                                                                                                                                                                                                                                                                                                                                                                                                                            422 
                                    13        23        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        |-
           KAT1_HUMAN     4 QLQARRLDGIDYNPWVEFVKLASEHDVVNLGQGFPDFPPPDFAVEAFQHAVSGDFMLNQYTKTFGYPPLTKILASFFGELLGQEIDPLRNVLVTVGGYGALFTAFQALVDEGDEVIIIEPFFDCYEPMTMMAGGRPVFVSLKPGPIQNGELGSSSNWQLDPMELAGKFTSRTKALVLNTPNNPLGKVFSREELELVASLCQQHDVVCITDEVYQWMVYDGHQHISIASLPGMWERTLTIGSAGKTFSATGWKVGWVLGPDHIMKHLRTVHQNSVFHCPTQSQAAVAESFEREQLLFRQPSSYFVQFPQAMQRCRDHMIRSLQSVGLKPIIPQGSYFLITDISDFKRKMPDLPGAVDEPYDRRFVKWMIKNKGLVAIPVSIFYSVPHQKHFDHYIRFCFVKDEATLQAMDEKLRKWKVEL-   -
               SCOP domains d1w7ma_ A: Kynurenine--oxoglutarate transaminase I                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------1w7mA02 A:44-301 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                              ------------------------------------------------------------------------------------------------------------------------ - CATH domains
               Pfam domains ------------------------Aminotran_1_2-1w7mA01 A:28-415                                                                                                                                                                                                                                                                                                                                                                      ------ - Pfam domains
         Sec.struct. author ...hhhhh....hhhhhhhhhh.....ee..........hhhhhhhhhhhh..hhhhhh......hhhhhhhhhhhhhhhhh...hhhhheeeehhhhhhhhhhhhhhh....eeeeee....hhhhhhhhh..eeeeee.....---...ee.hhh..hhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhhhh.eeeee..............hhhhh..hhh.eeeeeehhhhh.hhhhh.eeee.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeee.....eeeeehhhhhhhh.........hhhhhhhhhhhhhh.ee.ee.hhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhhh.-. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.5b      -------------------------------------------------Exon 1.9b  PDB: A:68-117 UniProt: 68-117          Exon 1.10  PDB: A:118-146    Exon 1.11c  PDB: A:147-189 (gaps)          Exon 1.12  PDB: A:190-230                -------------------------Exon 1.14  PDB: A:256-285     Exon 1.15a  PDB: A:286-348 UniProt: 286-348                    --------------------------Exon 1.17  PDB: A:375-403    Exon 1.18d         - Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.6  PDB: A:18-67 UniProt: 18-67             ------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.13c  PDB: A:230-255--------------------------------------------------------------------------------------------Exon 1.16a  PDB: A:348-374 ------------------------------------------------- Transcript 1 (2)
                 1w7m A   4 QLQARRLDGIDYNPWVEFVKLASEHDVVNLGQGFPDFPPPDFAVEAFQHAVSGDFMLNQYTKTFGYPPLTKILASFFGELLGQEIDPLRNVLVTVGGYGALFTAFQALVDEGDEVIIIEPFFDCYEPMTMMAGGRPVFVSLKPGP---GELGSSSNWQLDPMELAGKFTSRTKALVLNTPNNPLGKVFSREELELVASLCQQHDVVCITDEVYQWMVYDGHQHISIASLPGMWERTLTIGSAGKTFSATGWKVGWVLGPDHIMKHLRTVHQNSVFHCPTQSQAAVAESFEREQLLFRQPSSYFVQFPQAMQRCRDHMIRSLQSVGLKPLIPQGSYFLITDISDFKRKMPDLPGAVDEPYDRRFVKWMIKNKGLVAIPVSIFYSVPHQKHFDHYIRFCFVKDEATLQAMDEKLRKWKVE-F 914
                                    13        23        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       914
                                                                                                                                                                          148 152                                                                                                                                                                                                                                                                          421 |
                                                                                                                                                                                                                                                                                                                                                                                                                                                             914

   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, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A   (KAT1_HUMAN | Q16773)
molecular function
    GO:0047945    L-glutamine:pyruvate aminotransferase activity    Catalysis of the reaction: L-glutamine + pyruvate = 2-oxoglutaramate + L-alanine.
    GO:0047312    L-phenylalanine:pyruvate aminotransferase activity    Catalysis of the reaction: pyruvate + L-phenylalanine = phenylpyruvate + L-alanine.
    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:0047804    cysteine-S-conjugate beta-lyase activity    Catalysis of the reaction: RS-CH2-CH(NH3+)COO- = RSH + NH3 + pyruvate.
    GO:0047316    glutamine-phenylpyruvate transaminase activity    Catalysis of the reaction: keto-phenylpyruvate + L-glutamine = 2-oxoglutaramate + L-phenylalanine.
    GO:0016212    kynurenine-oxoglutarate transaminase activity    Catalysis of the reaction: L-kynurenine + 2-oxoglutarate = 4-(2-aminophenyl)-2,4-dioxobutanoate + L-glutamate.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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.
    GO:0008483    transaminase activity    Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    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:0006559    L-phenylalanine catabolic process    The chemical reactions and pathways resulting in the breakdown of phenylalanine, 2-amino-3-phenylpropanoic acid.
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0006575    cellular modified amino acid metabolic process    The chemical reactions and pathways involving compounds derived from amino acids, organic acids containing one or more amino substituents.
    GO:0070189    kynurenine metabolic process    The chemical reactions and pathways involving kynurenine, the amino acid 3-(2-aminobenzoyl)-alanine.
    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.
    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: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
        KAT1_HUMAN | Q167731w7l 1w7n 3fvs 3fvu 3fvx 4wlh 4wlj 4wp0

(-) Related Entries Specified in the PDB File

1w7l CRYSTAL STRUCTURE OF HUMAN KYNURENINE AMINOTRANSFERASE I
1w7n CRYSTAL STRUCTURE OF HUMAN KYNURENINE AMINOTRANSFERASE I IN PMP FORM