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(-) Description

Title :  CRYSTAL STRUCTURE OF PREPHENATE DEHYDROGENASE FROM A. AEOLICUS WITH HPP AND NADH
 
Authors :  W. Sun, D. Shahinas, D. Christendat
Date :  01 Mar 09  (Deposition) - 10 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Tyra, Hpp, Nadh, Alpha-Beta, 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: A, B, C, D
    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): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1ENO2Ligand/Ion3-(4-HYDROXY-PHENYL)PYRUVIC ACID
2NAI4Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ENO1Ligand/Ion3-(4-HYDROXY-PHENYL)PYRUVIC ACID
2NAI2Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1ENO1Ligand/Ion3-(4-HYDROXY-PHENYL)PYRUVIC ACID
2NAI2Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:37 , VAL A:38 , GLY A:39 , PHE A:40 , MET A:41 , ASP A:62 , ILE A:63 , ASN A:64 , SER A:67 , SER A:98 , SER A:99 , PRO A:100 , VAL A:101 , ARG A:102 , THR A:103 , ILE A:107 , GLN A:124 , SER A:126 , PRO A:148 , ALA A:150 , GLY A:151 , SER A:155 , GLY A:156 , GLU A:234 , MET A:258 , HOH A:1030 , HOH A:1032BINDING SITE FOR RESIDUE NAI A 2372
2AC2SOFTWARESER B:126 , HIS B:147 , ALA B:150 , GLY B:151 , THR B:152 , GLU B:153 , HIS B:217 , ARG B:250 , HOH B:1004 , HOH B:1015 , HOH B:1073 , NAI B:3372 , GLY D:242 , GLY D:243 , GLY D:244BINDING SITE FOR RESIDUE ENO B 3168
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 , SER B:126 , PRO B:148 , ALA B:150 , THR B:152 , SER B:155 , GLY B:156 , MET B:258 , HOH B:1003 , HOH B:1010 , HOH B:1017 , HOH B:1028 , HOH B:1044 , ENO B:3168BINDING SITE FOR RESIDUE NAI B 3372
4AC4SOFTWAREGLY A:242 , GLY A:243 , GLY A:244 , SER C:126 , HIS C:147 , ALA C:150 , GLY C:151 , THR C:152 , GLU C:153 , HIS C:217 , ARG C:250 , ILE C:251 , HOH C:1014 , HOH C:1020 , HOH C:1023 , NAI C:4372BINDING SITE FOR RESIDUE ENO C 3167
5AC5SOFTWAREGLY C:37 , VAL C:38 , GLY C:39 , PHE C:40 , MET C:41 , ASP C:62 , SER C:67 , SER C:98 , SER C:99 , PRO C:100 , VAL C:101 , THR C:103 , ILE C:107 , GLN C:124 , GLY C:125 , SER C:126 , PRO C:148 , ALA C:150 , THR C:152 , SER C:155 , GLY C:156 , MET C:258 , HOH C:1005 , HOH C:1018 , HOH C:1066 , HOH C:1082 , HOH C:1223 , ENO C:3167BINDING SITE FOR RESIDUE NAI C 4372
6AC6SOFTWAREGLY D:37 , VAL D:38 , GLY D:39 , PHE D:40 , MET D:41 , TYR D:61 , ASP D:62 , ILE D:63 , SER D:67 , SER D:98 , SER D:99 , PRO D:100 , VAL D:101 , THR D:103 , ILE D:107 , GLN D:124 , SER D:126 , GLU D:153 , LYS D:154 , SER D:155 , GLY D:156 , MET D:258 , HOH D:1054BINDING SITE FOR RESIDUE NAI D 1372

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GGO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3GGO)

(-) 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..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhh....eee...hhhhhhh..eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhh..ee.eee.......hhhhh........eeee......hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ggo 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:282
 aligned with O67636_AQUAE | O67636 from UniProtKB/TrEMBL  Length:311

    Alignment length:282
                                    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    28 LSMQNVLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKRME 309
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhh....eee.hhhhhhhhh..eeee..hhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhh..ee.eee.......hhhhh........eeee......hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ggo B  28 LSMQNVLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKRME 309
                                    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 .......eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhh....eee.hhhhhhhhh..eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhh..ee.eee.......hhhhh........eeee......hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ggo 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:282
 aligned with O67636_AQUAE | O67636 from UniProtKB/TrEMBL  Length:311

    Alignment length:282
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306  
         O67636_AQUAE    27 SLSMQNVLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKRM 308
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhh.....ee...hhhhhhh..eeee..hhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhh..ee.eee.......hhhhh........eeee......hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ggo D  27 SLSMQNVLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKRM 308
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306
   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 3GGO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 3ggg 3ggp

(-) Related Entries Specified in the PDB File

3ggg TYROSINE BOUND TYRA STRUCTURE
3ggp