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(-) Description

Title :  CRYSTAL STRUCTURE OF PYROCOCCUS HORIKOSHII KYNURENINE AMINOTRANSFERASE IN COMPLEX WITH PMP, GLA, 4AD, 2OG, GLU AND KYA
 
Authors :  K. Okada, C. Angkawidjaja, Y. Koga, S. Kanaya
Date :  28 Jul 14  (Deposition) - 24 Sep 14  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Aminotransferase, Kyn Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Okada, C. Angkawidjaja, Y. Koga, S. Kanaya
Crystal Structure Of Pyrococcus Horikoshii Kynurenine Aminotransferase In Complex With Pmp, Gla, 4Ad, 2Og, Glu An Kya
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN PH0207
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3) CODON PLUS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: KAT, PH0207
    Organism Scientific: PYROCOCCUS HORIKOSHII OT3
    Organism Taxid: 70601
    Strain: OT3

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 10)

Asymmetric/Biological Unit (6, 10)
No.NameCountTypeFull Name
13EE2Ligand/Ion4-(2-AMINOPHENYL)-2,4-DIOXOBUTANOIC ACID
2AKG2Ligand/Ion2-OXOGLUTARIC ACID
3G9A2Ligand/Ion(2E)-PENT-2-ENEDIOIC ACID
4GLU1Mod. Amino AcidGLUTAMIC ACID
5KYA1Ligand/Ion4-HYDROXYQUINOLINE-2-CARBOXYLIC ACID
6PMP2Ligand/Ion4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:128 , SER A:129 , GLN A:130 , TYR A:154 , ASN A:208 , ASP A:236 , PRO A:238 , TYR A:239 , THR A:266 , SER A:268 , LYS A:269 , ARG A:276 , G9A A:503 , TYR C:94BINDING SITE FOR RESIDUE PMP A 501
02AC2SOFTWARETYR A:115 , ASP A:237 , PRO A:238 , TYR A:239 , GLY A:240 , GLU A:241 , LEU A:242 , TYR A:263 , GLY A:265 , THR A:266 , ILE A:270 , HOH A:614 , HOH A:878 , HOH A:879 , HOH A:880BINDING SITE FOR RESIDUE AKG A 502
03AC3SOFTWAREGLY A:64 , TYR A:154 , LEU A:155 , ALA A:156 , ASN A:208 , TYR A:239 , ARG A:400 , PMP A:501 , 3EE A:504 , HOH A:798BINDING SITE FOR RESIDUE G9A A 503
04AC4SOFTWAREARG A:47 , GLY A:64 , LEU A:65 , ARG A:400 , G9A A:503 , HOH A:641 , HOH A:881 , HOH A:910 , TYR C:94BINDING SITE FOR RESIDUE 3EE A 504
05AC5SOFTWARESER A:44 , VAL A:46 , LEU A:155 , VAL A:384 , ALA A:388 , ARG A:393 , HOH A:759 , HOH A:822 , HOH A:877BINDING SITE FOR RESIDUE GLU A 505
06AC6SOFTWARETYR A:94 , GLY C:128 , SER C:129 , GLN C:130 , TYR C:154 , VAL C:203 , ASN C:208 , ASP C:236 , PRO C:238 , TYR C:239 , THR C:266 , SER C:268 , LYS C:269 , ARG C:276 , G9A C:503BINDING SITE FOR RESIDUE PMP C 501
07AC7SOFTWARETYR C:115 , ASP C:237 , GLY C:240 , GLU C:241 , LYS C:251 , TYR C:263 , GLY C:265 , THR C:266 , ILE C:270 , TRP C:279 , HOH C:893 , HOH C:894 , HOH C:900BINDING SITE FOR RESIDUE AKG C 502
08AC8SOFTWAREARG C:47 , GLY C:64 , TYR C:154 , LEU C:155 , ALA C:156 , ASN C:208 , TYR C:239 , LYS C:269 , ARG C:400 , PMP C:501 , 3EE C:504 , HOH C:754 , HOH C:755BINDING SITE FOR RESIDUE G9A C 503
09AC9SOFTWARETYR A:94 , GLY C:63 , GLY C:64 , LEU C:65 , ARG C:400 , G9A C:503 , HOH C:659 , HOH C:896 , HOH C:897 , HOH C:1017BINDING SITE FOR RESIDUE 3EE C 504
10BC1SOFTWARESER C:44 , VAL C:46 , ARG C:47 , LEU C:155 , GLN C:159 , LYS C:370 , ALA C:388 , ARG C:393 , HOH C:842 , HOH C:1010BINDING SITE FOR RESIDUE KYA C 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WX9)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:151 -Pro A:152
2Asn A:208 -Pro A:209
3Ala C:151 -Pro C:152
4Asn C:208 -Pro C:209

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WX9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WX9)

(-) Exons   (0, 0)

(no "Exon" information available for 3WX9)

(-) 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:404
 aligned with O57946_PYRHO | O57946 from UniProtKB/TrEMBL  Length:428

    Alignment length:404
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424    
         O57946_PYRHO    25 SMLGDVERFFSKKALEMRASEVRELLKLVETSDIISLAGGLPNPKTFPKEIIRDILVEIMEKYADKALQYGTTKGFTPLRETLMKWLGKRYGISQDNDIMITSGSQQALDLIGRVFLNPGDIVVVEAPTYLAALQAFNFYEPQYIQIPLDDEGMKVEILEEKLKELKSQGKKVKVVYTVPTFQNPAGVTMNEDRRKYLLELASEYDFIVVEDDPYGELRYSGNPEKKIKALDNEGRVIYLGTFSKILAPGFRIGWMVGDPGIIRKMEIAKQSTDLCTNVFGQVVAWRYVDGGYLEKHIPEIRKFYKPRRDAMLEALEEFMPEGVKWTKPEGGMFIWVTLPDGIDSKKMLERAIKKGVAYVPGEAFYAHRDVKNTMRLNFTYVDEDKIMEGIKRLAETIKEELKA 428
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh..hhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh...eeeeeeee..eehhhhhhhhhhhhhhh.....eeee............hhhhhhhhhhhhhhhh.eeeee...............hhhhh....eeeeee.....hhhhh.eeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.......eeeee.....hhhhhhhhhhhh.ee.ee.hhhh.......eeeee......hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wx9 A  25 SMLGDVERFFSKKALEMRASEVRELLKLVETSDIISLAGGLPNPKTFPKEIIRDILVEIMEKYADKALQYGTTKGFTPLRETLMKWLGKRYGISQDNDIMITSGSQQALDLIGRVFLNPGDIVVVEAPTYLAALQAFNFYEPQYIQIPLDDEGMKVEILEEKLKELKSQGKKVKVVYTVPTFQNPAGVTMNEDRRKYLLELASEYDFIVVEDDPYGELRYSGNPEKKIKALDNEGRVIYLGTFSKILAPGFRIGWMVGDPGIIRKMEIAKQSTDLCTNVFGQVVAWRYVDGGYLEKHIPEIRKFYKPRRDAMLEALEEFMPEGVKWTKPEGGMFIWVTLPDGIDSKKMLERAIKKGVAYVPGEAFYAHRDVKNTMRLNFTYVDEDKIMEGIKRLAETIKEELKA 428
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424    


Chain C from PDB  Type:PROTEIN  Length:404
 aligned with O57946_PYRHO | O57946 from UniProtKB/TrEMBL  Length:428

    Alignment length:404
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424    
         O57946_PYRHO    25 SMLGDVERFFSKKALEMRASEVRELLKLVETSDIISLAGGLPNPKTFPKEIIRDILVEIMEKYADKALQYGTTKGFTPLRETLMKWLGKRYGISQDNDIMITSGSQQALDLIGRVFLNPGDIVVVEAPTYLAALQAFNFYEPQYIQIPLDDEGMKVEILEEKLKELKSQGKKVKVVYTVPTFQNPAGVTMNEDRRKYLLELASEYDFIVVEDDPYGELRYSGNPEKKIKALDNEGRVIYLGTFSKILAPGFRIGWMVGDPGIIRKMEIAKQSTDLCTNVFGQVVAWRYVDGGYLEKHIPEIRKFYKPRRDAMLEALEEFMPEGVKWTKPEGGMFIWVTLPDGIDSKKMLERAIKKGVAYVPGEAFYAHRDVKNTMRLNFTYVDEDKIMEGIKRLAETIKEELKA 428
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh...hhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh...eeeeeeee..eehhhhhhhhhhhhhhh...eeeeee............hhhhhhhhhhhhhhhh.eeeee..............hhhhhh....eeeeee.....hhhhh.eeeeehhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.......eeeee.....hhhhhhhhhhhh.ee.ee.hhhh.......eeeee......hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wx9 C  25 SMLGDVERFFSKKALEMRASEVRELLKLVETSDIISLAGGLPNPKTFPKEIIRDILVEIMEKYADKALQYGTTKGFTPLRETLMKWLGKRYGISQDNDIMITSGSQQALDLIGRVFLNPGDIVVVEAPTYLAALQAFNFYEPQYIQIPLDDEGMKVEILEEKLKELKSQGKKVKVVYTVPTFQNPAGVTMNEDRRKYLLELASEYDFIVVEDDPYGELRYSGNPEKKIKALDNEGRVIYLGTFSKILAPGFRIGWMVGDPGIIRKMEIAKQSTDLCTNVFGQVVAWRYVDGGYLEKHIPEIRKFYKPRRDAMLEALEEFMPEGVKWTKPEGGMFIWVTLPDGIDSKKMLERAIKKGVAYVPGEAFYAHRDVKNTMRLNFTYVDEDKIMEGIKRLAETIKEELKA 428
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424
   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 3WX9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WX9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WX9)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (O57946_PYRHO | O57946)
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: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: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.

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  O57946_PYRHO | O57946
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 Related Entries

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

UniProtKB/TrEMBL
        O57946_PYRHO | O57946: 1x0m 3aov 3aow 3ath 3av7

(-) Related Entries Specified in the PDB File

3av7 THE SAME PROTEIN COMPLEXED WITH GLUTACONIC ACID AND 4-(2- AMINOPHENYL)-2,4-DIOXOBUTANOATE .