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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A. AEOLICUS PREPHENATE DEHYDROGENASE IN COMPLEX WITH TYROSINE AND NAD+
 
Authors :  W. Sun, D. Shahinas, D. Christendat
Date :  27 Feb 09  (Deposition) - 10 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.21
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  B,D  (1x)
Biol. Unit 2:  A,C  (1x)
Keywords :  Dinucleotide Binding Fold, Beta-Alpha, Tyrosine-Bound, Nad, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Sun, D. Shahinas, J. Bonvin, W. Hou, M. S. Kimber, J. Turnbull, D. Christendat
The Crystal Structure Of Aquifex Aeolicus Prephenate Dehydrogenase Reveals The Mode Of Tyrosine Inhibition.
J. Biol. Chem. V. 284 13223 2009
PubMed-ID: 19279014  |  Reference-DOI: 10.1074/JBC.M806272200

(-) Compounds

Molecule 1 - PREPHENATE DEHYDROGENASE
    Chains: D, A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AQ_1755, TYRA
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Strain: VF5

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):  B D
Biological Unit 2 (1x): A C 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2TYR2Mod. Amino AcidTYROSINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2TYR1Mod. Amino AcidTYROSINE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2TYR1Mod. Amino AcidTYROSINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY D:37 , VAL D:38 , GLY D:39 , PHE D:40 , MET D:41 , ASP D:62 , ILE D:63 , SER D:67 , SER D:98 , SER D:99 , PRO D:100 , VAL D:101 , THR D:103 , PHE D:104 , ILE D:107 , GLN D:124 , SER D:126 , PRO D:148 , GLY D:151 , THR D:152 , SER D:155 , GLY D:156 , HOH D:1219BINDING SITE FOR RESIDUE NAD D 6686
2AC2SOFTWAREGLY A:37 , VAL A:38 , GLY A:39 , PHE A:40 , MET A:41 , ASP A:62 , ILE A:63 , SER A:67 , SER A:98 , SER A:99 , PRO A:100 , VAL A:101 , THR A:103 , ILE A:107 , GLN A:124 , SER A:126 , PRO A:148 , GLY A:151 , THR A:152 , SER A:155 , GLY A:156 , GLU A:234 , HOH A:1004 , HOH A:1022BINDING SITE FOR RESIDUE NAD A 3686
3AC3SOFTWAREGLY B:37 , VAL B:38 , GLY B:39 , PHE B:40 , MET B:41 , ASP B:62 , ILE B:63 , ASN B:64 , SER B:67 , SER B:98 , SER B:99 , PRO B:100 , VAL B:101 , THR B:103 , ILE B:107 , GLN B:124 , GLY B:125 , SER B:126 , PRO B:148 , ALA B:150 , GLY B:151 , THR B:152 , SER B:155 , GLY B:156 , MET B:258 , HOH B:1005 , HOH B:1023 , HOH B:1036 , HOH B:1065 , HOH B:1083 , TYR B:6959BINDING SITE FOR RESIDUE NAD B 4686
4AC4SOFTWARESER B:126 , HIS B:147 , GLY B:151 , THR B:152 , GLU B:153 , ARG B:250 , HOH B:1008 , HOH B:1019 , NAD B:4686 , GLY D:242 , GLY D:243BINDING SITE FOR RESIDUE TYR B 6959
5AC5SOFTWAREGLY C:37 , VAL C:38 , GLY C:39 , PHE C:40 , MET C:41 , ASP C:62 , ILE C:63 , ASN C:64 , SER C:67 , SER C:98 , SER C:99 , PRO C:100 , VAL C:101 , THR C:103 , ILE C:107 , GLN C:124 , SER C:126 , PRO C:148 , ALA C:150 , THR C:152 , SER C:155 , GLY C:156 , MET C:258 , HOH C:1018 , HOH C:1020 , HOH C:1043 , HOH C:1094 , TYR C:5959BINDING SITE FOR RESIDUE NAD C 5686
6AC6SOFTWAREGLY A:242 , GLY A:243 , SER C:126 , HIS C:147 , THR C:152 , ARG C:250 , ILE C:251 , HOH C:1003 , HOH C:1062 , NAD C:5686BINDING SITE FOR RESIDUE TYR C 5959

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:28 -Ser A:29

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3GGG)

(-) 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:285
 aligned with O67636_AQUAE | O67636 from UniProtKB/TrEMBL  Length:311

    Alignment length:285
                                    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     
         O67636_AQUAE    26 KSLSMQNVLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKRMEI 310
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee..hhhhhhhhhhhhh.....eeeee..hhhhhhhhhhh....eee.hhhhhhhhh..eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhh.eeee.......hhhhh........eeeee.....hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ggg A  26 KSLSMQNVLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKRMEI 310
                                    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     


Chain B from PDB  Type:PROTEIN  Length:290
 aligned with O67636_AQUAE | O67636 from UniProtKB/TrEMBL  Length:311

    Alignment length:290
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307
         O67636_AQUAE    18 KKNIIKILKSLSMQNVLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKR 307
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhh....eee....hhhhhh..eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhh..ee.eee.......hhhhh........eeee......hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ggg B  18 MKNIIKILKSLSMQNVLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKR 307
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307


Chain C from PDB  Type:PROTEIN  Length:281
 aligned with O67636_AQUAE | O67636 from UniProtKB/TrEMBL  Length:311

    Alignment length:281
                                    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 
         O67636_AQUAE    25 LKSLSMQNVLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKI 305
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhh....eee.hhhhhhhhh..eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhh..ee.eee.......hhhhh........eeee......hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ggg C  25 LKSLSMQNVLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKI 305
                                    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 


Chain D from PDB  Type:PROTEIN  Length:293
 aligned with O67636_AQUAE | O67636 from UniProtKB/TrEMBL  Length:311

    Alignment length:293
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307   
         O67636_AQUAE    18 KKNIIKILKSLSMQNVLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKRMEI 310
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh..eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhh....eee.hhhhhhhhh..eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhh..ee.eee.......hhhhh........eeee......hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ggg D  18 MKNIIKILKSLSMQNVLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKRMEI 310
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307
   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 3GGG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (O67636_AQUAE | O67636)
molecular function
    GO:0070403    NAD+ binding    Interacting selectively and non-covalently with the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0008977    prephenate dehydrogenase (NAD+) activity    Catalysis of the reaction: NAD(+) + prephenate = (4-hydroxyphenyl)pyruvate + CO(2) + NADH.
    GO:0004665    prephenate dehydrogenase (NADP+) activity    Catalysis of the reaction: NADP(+) + prephenate = (4-hydroxyphenyl)pyruvate + CO(2) + NADPH.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006571    tyrosine biosynthetic process    The chemical reactions and pathways resulting in the formation of tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid.

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 Related Entries

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

UniProtKB/TrEMBL
        O67636_AQUAE | O67636: 2g5c 3ggo 3ggp

(-) Related Entries Specified in the PDB File

3ggo 3ggp