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(-) Description

Title :  CRYSTAL STRUCTURE OF LYSN, ALPHA-AMINOADIPATE AMINOTRANSFERASE, FROM THERMUS THERMOPHILUS HB27
 
Authors :  T. Tomita, T. Miyazaki, T. Miyagawa, S. Fushinobu, T. Kuzuyama, M. Nishiyama
Date :  21 Feb 08  (Deposition) - 13 Jan 09  (Release) - 13 Jan 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Aminoadipate Aminotransferase, Thermus Thermophilus, Substrate Specifity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Tomita, T. Miyagawa, T. Miyazaki, S. Fushinobu, T. Kuzuyama, M. Nishiyama
Mechanism For Multiple-Substrates Recognition Of Alpha-Aminoadipate Aminotransferase From Thermus Thermophilus
Proteins 2008
PubMed-ID: 18831049  |  Reference-DOI: 10.1002/PROT.22245
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-AMINODIPATE AMINOTRANSFERASE
    Chains: A, B
    EC Number: 2.6.1.39
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-LYSN7
    Expression System Strain: BL21 CODON-PLUS(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LYSN
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Strain: HB27

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1N5F2Ligand/Ion(2S)-2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]HEXANEDIOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:22 , ARG A:23 , GLY A:39 , GLY A:40 , GLY A:99 , SER A:100 , GLN A:101 , TYR A:125 , ASN A:174 , ASP A:202 , TYR A:205 , SER A:235 , SER A:237 , LYS A:238 , ARG A:245 , ARG A:368 , TYR B:70BINDING SITE FOR RESIDUE N5F A 500
2AC2SOFTWARETYR A:70 , ILE B:22 , ARG B:23 , GLY B:39 , GLY B:40 , GLY B:99 , SER B:100 , GLN B:101 , TYR B:125 , ASN B:174 , ASP B:202 , TYR B:205 , SER B:235 , SER B:237 , LYS B:238 , ARG B:245 , ARG B:368BINDING SITE FOR RESIDUE N5F B 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:122 -Pro A:123
2Asn A:174 -Pro A:175
3Ala B:122 -Pro B:123
4Asn B:174 -Pro B:175

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CBF)

(-) 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:392
 aligned with LYSN_THET2 | Q72LL6 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:392
                                    14        24        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  
           LYSN_THET2     5 SWSEAFGKGAGRIQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREKGEVALQYSPTEGYAPLRAFVAEWIGVRPEEVLITTGSQQALDLVGKVFLDEGSPVLLEAPSYMGAIQAFRLQGPRFLTVPAGEEGPDLDALEEVLKRERPRFLYLIPSFQNPTGGLTPLPARKRLLQMVMERGLVVVEDDAYRELYFGEARLPSLFELAREAGYPGVIYLGSFSKVLSPGLRVAFAVAHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEGFSERLERVRRVYREKAQAMLHALDREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFFANGGGENTLRLSYATLDREGIAEGVRRLGRALKGLLAL 396
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.hhh.eeee.hhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh...eeeeeeee..eehhhhhhhhhhhh....eee............hhhhhhhhhhhhhhhh..eeee..............hhhhhhhhhh...eeeeee...........eeee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.......eeeee.....hhhhhhhhhhhh.eeeee.hhhh.......eeeee....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cbf A   5 SWSEAFGKGAGRIQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREKGEVALQYSPTEGYAPLRAFVAEWIGVRPEEVLITTGSQQALDLVGKVFLDEGSPVLLEAPSYMGAIQAFRLQGPRFLTVPAGEEGPDLDALEEVLKRERPRFLYLIPSFQNPTGGLTPLPARKRLLQMVMERGLVVVEDDAYRELYFGEARLPSLFELAREAGYPGVIYLGSFSKVLSPGLRVAFAVAHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEGFSERLERVRRVYREKAQAMLHALDREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFFANGGGENTLRLSYATLDREGIAEGVRRLGRALKGLLAL 396
                                    14        24        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  


Chain B from PDB  Type:PROTEIN  Length:392
 aligned with LYSN_THET2 | Q72LL6 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:392
                                    14        24        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  
           LYSN_THET2     5 SWSEAFGKGAGRIQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREKGEVALQYSPTEGYAPLRAFVAEWIGVRPEEVLITTGSQQALDLVGKVFLDEGSPVLLEAPSYMGAIQAFRLQGPRFLTVPAGEEGPDLDALEEVLKRERPRFLYLIPSFQNPTGGLTPLPARKRLLQMVMERGLVVVEDDAYRELYFGEARLPSLFELAREAGYPGVIYLGSFSKVLSPGLRVAFAVAHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEGFSERLERVRRVYREKAQAMLHALDREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFFANGGGENTLRLSYATLDREGIAEGVRRLGRALKGLLAL 396
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.hhh.eeeehhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh...eeeeeeee..eehhhhhhhhhhhh....eee............hhhhhhhhhhhhhhhh..eeee..............hhhhhhhhhh...eeeeee...........eeee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.......eeeee.....hhhhhhhhhhhh.eeeee.hhhh.......eeeee....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cbf B   5 SWSEAFGKGAGRIQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREKGEVALQYSPTEGYAPLRAFVAEWIGVRPEEVLITTGSQQALDLVGKVFLDEGSPVLLEAPSYMGAIQAFRLQGPRFLTVPAGEEGPDLDALEEVLKRERPRFLYLIPSFQNPTGGLTPLPARKRLLQMVMERGLVVVEDDAYRELYFGEARLPSLFELAREAGYPGVIYLGSFSKVLSPGLRVAFAVAHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEGFSERLERVRRVYREKAQAMLHALDREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFFANGGGENTLRLSYATLDREGIAEGVRRLGRALKGLLAL 396
                                    14        24        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
   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 3CBF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (LYSN_THET2 | Q72LL6)
molecular function
    GO:0047536    2-aminoadipate transaminase activity    Catalysis of the reaction: 2-oxoglutarate + L-2-aminoadipate = 2-oxoadipate + L-glutamate.
    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.
    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: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:0019878    lysine biosynthetic process via aminoadipic acid    The chemical reactions and pathways resulting in the formation of lysine by the aminoadipic pathway.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LYSN_THET2 | Q72LL6: 2egy 2z1y 2zp7 2zyj

(-) Related Entries Specified in the PDB File

2dtv LEUCINE AND PYRIDOXAL 5'-PHOSPHATE COMPLEXED FORM OF THE SAME PROTEIN.
2egy PYRIDOXAL 5'-PHOSPHATE COMPLEXED FORM OF THE SAME PROTEIN.
2z1y N-(5'-PHOSPHOPYRIDOXYL)-L-LEUCINE COMPLEXED FORM OF THE SAME PROTEIN.