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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE KYNURENINE AMINOTRANSFERASE III, PLP-BOUND FORM
 
Authors :  Q. Han, R. Robinson, T. Cai, D. A. Tagle, J. Li
Date :  05 Aug 08  (Deposition) - 30 Dec 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.59
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha Beta Protein, Plp Dependent Protein, Aminotransferase, Lyase, Pyridoxal Phosphate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Han, H. Robinson, T. Cai, D. A. Tagle, J. Li
Biochemical And Structural Properties Of Mouse Kynurenine Aminotransferase Iii.
Mol. Cell. Biol. V. 29 784 2009
PubMed-ID: 19029248  |  Reference-DOI: 10.1128/MCB.01272-08

(-) Compounds

Molecule 1 - KYNURENINE-OXOGLUTARATE TRANSAMINASE 3
    Chains: A, B
    EC Number: 2.6.1.7, 4.4.1.13
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Plasmid: PBLUEBAC4.5
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Gene: CCBL2, KAT3
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: KYNURENINE-OXOGLUTARATE TRANSAMINASE III, KYNURENINE AMINOTRANSFERASE III, KATIII, CYSTEINE-S-CONJUGATE BETA-LYASE 2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1GOL10Ligand/IonGLYCEROL
2LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:71 , GLY A:72 , TYR A:160 , ASN A:219 , PHE A:373 , ARG A:430 , GOL A:457BINDING SITE FOR RESIDUE GOL A 456
02AC2SOFTWARETRP A:54 , TYR A:136 , TYR A:160 , ASP A:161 , GOL A:456BINDING SITE FOR RESIDUE GOL A 457
03AC3SOFTWAREARG A:180 , SER A:181 , THR A:195 , ASP A:197 , ARG B:180 , SER B:181 , LYS B:182 , THR B:195 , ASP B:197BINDING SITE FOR RESIDUE GOL A 458
04AC4SOFTWAREGLN A:231 , ASP A:235 , PRO A:267BINDING SITE FOR RESIDUE GOL A 459
05AC5SOFTWAREGLU A:152 , SER A:203 , LYS A:204BINDING SITE FOR RESIDUE GOL A 460
06AC6SOFTWAREASP A:241 , GLU A:271 , ARG A:272 , HIS A:298BINDING SITE FOR RESIDUE GOL A 461
07AC7SOFTWARETYR A:312 , ASN B:52 , TRP B:54 , TYR B:136 , ASP B:161 , GOL B:457BINDING SITE FOR RESIDUE GOL B 456
08AC8SOFTWARETRP B:54 , GLN B:71 , GLY B:72 , ASN B:219 , TYR B:250 , PHE B:373 , ARG B:430 , GOL B:456BINDING SITE FOR RESIDUE GOL B 457
09AC9SOFTWAREILE B:118 , GLU B:251 , TRP B:252 , HOH B:494BINDING SITE FOR RESIDUE GOL B 458
10BC1SOFTWAREGLN B:231 , ASP B:235 , VAL B:238 , PRO B:267BINDING SITE FOR RESIDUE GOL B 459

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E2F)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Val A:157 -Pro A:158
2Thr A:216 -Pro A:217
3Asn A:219 -Pro A:220
4Val B:157 -Pro B:158
5Thr B:216 -Pro B:217
6Asn B:219 -Pro B:220

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E2F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3E2F)

(-) Exons   (0, 0)

(no "Exon" information available for 3E2F)

(-) Sequences/Alignments

Asymmetric/Biological 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:410
 aligned with KAT3_MOUSE | Q71RI9 from UniProtKB/Swiss-Prot  Length:455

    Alignment length:410
                                    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       411       421       431       441       451
           KAT3_MOUSE    42 NAKRIEGLDSNVWVEFTKLAADPSVVNLGQGFPDISPPSYVKEELSKAAFIDNMNQYTRGFGHPALVKALSCLYGKIYQRQIDPNEEILVAVGAYGSLFNSIQGLVDPGDEVIIMVPFYDCYEPMVRMAGAVPVFIPLRSKPTDGMKWTSSDWTFDPRELESKFSSKTKAIILNTPHNPLGKVYTRQELQVIADLCVKHDTLCISDEVYEWLVYTGHTHVKIATLPGMWERTITIGSAGKTFSVTGWKLGWSIGPAHLIKHLQTVQQNSFYTCATPLQAALAEAFWIDIKRMDDPECYFNSLPKELEVKRDRMVRLLNSVGLKPIVPDGGYFIIADVSSLGADLSDMNSDEPYDYKFVKWMTKHKKLTAIPVSAFCDSKSKPHFEKLVRFCFIKKDSTLDAAEEIFRAWN 451
               SCOP domains d3e2fa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh....hhhhhhhhhh.....ee..........hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh........eeeehhhhhhhhhhhhhhh....eeeeee....hhhhhhhhh..eeeeee.ee........hhh.ee.hhhhhhh.....eeeeeee..........hhhhhhhhhhhhhhh..eeeee..............hhhhh..hhh.eeeeeehhhhhhhhhhh.eeee.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...eee......eeeee...............hhhhhhhhhhhhhhhee.ee.hhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e2f A  42 NAKRIEGLDSNVWVEFTKLAADPSVVNLGQGFPDISPPSYVKEELSKAAFIDNMNQYTRGFGHPALVKALSCLYGKIYQRQIDPNEEILVAVGAYGSLFNSIQGLVDPGDEVIIMVPFYDCYEPMVRMAGAVPVFIPLRSKPTDGMKWTSSDWTFDPRELESKFSSKTKAIILNTPHNPLGKVYTRQELQVIADLCVKHDTLCISDEVYEWLVYTGHTHVKIATLPGMWERTITIGSAGkTFSVTGWKLGWSIGPAHLIKHLQTVQQNSFYTCATPLQAALAEAFWIDIKRMDDPECYFNSLPKELEVKRDRMVRLLNSVGLKPIVPDGGYFIIADVSSLGADLSDMNSDEPYDYKFVKWMTKHKKLTAIPVSAFCDSKSKPHFEKLVRFCFIKKDSTLDAAEEIFRAWN 451
                                    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       411       421       431       441       451
                                                                                                                                                                                                                                                                         281-LLP                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:410
 aligned with KAT3_MOUSE | Q71RI9 from UniProtKB/Swiss-Prot  Length:455

    Alignment length:410
                                    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       411       421       431       441       451
           KAT3_MOUSE    42 NAKRIEGLDSNVWVEFTKLAADPSVVNLGQGFPDISPPSYVKEELSKAAFIDNMNQYTRGFGHPALVKALSCLYGKIYQRQIDPNEEILVAVGAYGSLFNSIQGLVDPGDEVIIMVPFYDCYEPMVRMAGAVPVFIPLRSKPTDGMKWTSSDWTFDPRELESKFSSKTKAIILNTPHNPLGKVYTRQELQVIADLCVKHDTLCISDEVYEWLVYTGHTHVKIATLPGMWERTITIGSAGKTFSVTGWKLGWSIGPAHLIKHLQTVQQNSFYTCATPLQAALAEAFWIDIKRMDDPECYFNSLPKELEVKRDRMVRLLNSVGLKPIVPDGGYFIIADVSSLGADLSDMNSDEPYDYKFVKWMTKHKKLTAIPVSAFCDSKSKPHFEKLVRFCFIKKDSTLDAAEEIFRAWN 451
               SCOP domains d3e2fb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh....hhhhhhhhhhh....ee..........hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh........eeeeehhhhhhhhhhhhhh....eeeeee....hhhhhhhhh..eeeeee.ee........hhh.ee.hhhhhhhh....eeeeeee..........hhhhhhhhhhhhhhhh.eeeee..............hhhhh......eeeeeehhhhhhhhhh.eeeee.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..eee......eeeee...............hhhhhhhhhhhhhhhee.ee.hhhh...hhhhh..eeeee...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e2f B  42 NAKRIEGLDSNVWVEFTKLAADPSVVNLGQGFPDISPPSYVKEELSKAAFIDNMNQYTRGFGHPALVKALSCLYGKIYQRQIDPNEEILVAVGAYGSLFNSIQGLVDPGDEVIIMVPFYDCYEPMVRMAGAVPVFIPLRSKPTDGMKWTSSDWTFDPRELESKFSSKTKAIILNTPHNPLGKVYTRQELQVIADLCVKHDTLCISDEVYEWLVYTGHTHVKIATLPGMWERTITIGSAGkTFSVTGWKLGWSIGPAHLIKHLQTVQQNSFYTCATPLQAALAEAFWIDIKRMDDPECYFNSLPKELEVKRDRMVRLLNSVGLKPIVPDGGYFIIADVSSLGADLSDMNSDEPYDYKFVKWMTKHKKLTAIPVSAFCDSKSKPHFEKLVRFCFIKKDSTLDAAEEIFRAWN 451
                                    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       411       421       431       441       451
                                                                                                                                                                                                                                                                         281-LLP
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3E2F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E2F)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (KAT3_MOUSE | Q71RI9)
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:0047804    cysteine-S-conjugate beta-lyase activity    Catalysis of the reaction: RS-CH2-CH(NH3+)COO- = RSH + NH3 + pyruvate.
    GO:0047315    kynurenine-glyoxylate transaminase activity    Catalysis of the reaction: L-kynurenine + glyoxylate = 4-(2-aminophenyl)-2,4-dioxobutanoate + glycine.
    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: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:0006103    2-oxoglutarate metabolic process    The chemical reactions and pathways involving oxoglutarate, the dianion of 2-oxoglutaric acid. It is a key constituent of the TCA cycle and a key intermediate in amino-acid metabolism.
    GO:0097052    L-kynurenine metabolic process    The chemical reactions and pathways involving L-kynurenine, the L-enantiomer of the amino acid kynurenine (3-(2-aminobenzoyl)-alanine).
    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:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
    GO:0070189    kynurenine metabolic process    The chemical reactions and pathways involving kynurenine, the amino acid 3-(2-aminobenzoyl)-alanine.
cellular component
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KAT3_MOUSE | Q71RI9: 2zjg 3e2y 3e2z

(-) Related Entries Specified in the PDB File

3e2y CRYSTAL STRUCTURE OF MOUSE KYNURENINE AMINOTRANSFERASE III IN COMPLEX WITH GLUTAMINE
3e2z CRYSTAL STRUCTURE OF MOUSE KYNURENINE AMINOTRANSFERASE III IN COMPLEX WITH KYNURENINE