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(-) Description

Title :  CRYSTAL STRUCTURE OF PREPHENATE DEHYDROGENASE FROM AQUIFEX AEOLICUS
 
Authors :  W. Sun, S. Singh, R. Zhang, J. L. Turnbull, D. Christendat
Date :  22 Feb 06  (Deposition) - 07 Mar 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Prephenate Dehydrogenase, Tyra, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Sun, S. Singh, R. Zhang, J. L. Turnbull, D. Christendat
Crystal Structure Of Prephenate Dehydrogenase From Aquifex Aeolicus: Insights Into The Catalytic Mechanism
J. Biol. Chem. V. 281 12919 2006
PubMed-ID: 16513644  |  Reference-DOI: 10.1074/JBC.M511986200

(-) Compounds

Molecule 1 - PREPHENATE DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.3.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 224324
    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, 33)

Asymmetric Unit (2, 33)
No.NameCountTypeFull Name
1MSE29Mod. Amino AcidSELENOMETHIONINE
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (2, 17)
No.NameCountTypeFull Name
1MSE15Mod. Amino AcidSELENOMETHIONINE
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 2 (2, 16)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:37 , VAL A:38 , GLY A:39 , PHE A:40 , MSE A:41 , TYR A:61 , 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 , ALA A:150 , GLY A:151 , GLU A:153 , LYS A:154 , SER A:155 , GLY A:156 , HOH A:3692BINDING SITE FOR RESIDUE NAD A 3686
2AC2SOFTWAREGLY B:37 , VAL B:38 , GLY B:39 , PHE B:40 , MSE B:41 , TYR B:61 , ASP B:62 , ILE B:63 , SER B:67 , SER B:98 , SER B:99 , PRO B:100 , VAL B:101 , ILE B:107 , GLN B:124 , SER B:126 , THR B:152 , LYS B:154 , SER B:155 , GLY B:156 , HOH B:4687 , HOH B:4727BINDING SITE FOR RESIDUE NAD B 4686
3AC3SOFTWAREGLY C:37 , VAL C:38 , GLY C:39 , PHE C:40 , MSE C:41 , TYR C:61 , 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 , GLY C:151 , THR C:152 , GLY C:156 , MSE C:258 , HOH C:5689 , HOH C:5692 , HOH C:5800BINDING SITE FOR RESIDUE NAD C 5686
4AC4SOFTWAREGLY D:37 , VAL D:38 , GLY D:39 , PHE D:40 , MSE D:41 , TYR D:61 , ASP D:62 , ILE D:63 , ASN D:64 , SER D:67 , SER D:98 , SER D:99 , PRO D:100 , VAL D:101 , ILE D:107 , GLN D:124 , SER D:126 , ALA D:150 , GLY D:151 , THR D:152 , GLY D:156 , MSE D:258 , HOH D:6691 , HOH D:6694 , HOH D:6717 , HOH D:6725 , HOH D:6797BINDING SITE FOR RESIDUE NAD D 6686

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2G5C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2G5C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2G5C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2G5C)

(-) Exons   (0, 0)

(no "Exon" information available for 2G5C)

(-) 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:278
 aligned with O67636_AQUAE | O67636 from UniProtKB/TrEMBL  Length:311

    Alignment length:281
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309 
         O67636_AQUAE    30 MQNVLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKRMEI 310
               SCOP domains d2g5ca2 A:30-200 Prephenate dehydrogenase TyrA                                                                                                                             d2g5ca1 A:201-310 Prephenate dehydrogenase TyrA                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhh....eee.hhhhhhhh...eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhh..ee.eeee......hhhhh........eeee......hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh...hhhhh---...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g5c A  30 mQNVLIVGVGFmGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVmLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYmSPELHDYVFGVVSHLPHAVAFALVDTLIHmSTPEVDLFKYPGGGFKDF---AKSDPImWRDIFLENKENVmKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKRmEI 310
                            |       39 |      49        59        69        79        89      | 99       109       119       129       139       149       159       169       179       189       199|      209       219       229|      239        |-  |    259       269 |     279       289       299       309 
                            |         41-MSE                                                 96-MSE                                                                                                 200-MSE                       230-MSE           248 252     |          271-MSE                              308-MSE
                           30-MSE                                                                                                                                                                                                                             258-MSE                                                


Chain B from PDB  Type:PROTEIN  Length:280
 aligned with O67636_AQUAE | O67636 from UniProtKB/TrEMBL  Length:311

    Alignment length:280
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310
         O67636_AQUAE    31 QNVLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKRMEI 310
               SCOP domains d2g5cb2 B:31-200 Prephenate dehydrogenase TyrA                                                                                                                            d2g5cb1 B:201-310 Prephenate dehydrogenase TyrA                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhh....eee.hhhhhhhh...eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhh..ee.eee.......hhhhh........eeee......hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g5c B  31 QNVLIVGVGFmGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVmLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYmSPELHDYVFGVVSHLPHAVAFALVDTLIHmSTPEVDLFKYPGGGFKDFTRIAKSDPImWRDIFLENKENVmKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKRmEI 310
                                    40|       50        60        70        80        90     | 100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270|      280       290       300       310
                                     41-MSE                                                 96-MSE                                                                                                 200-MSE                       230-MSE                     258-MSE      271-MSE                              308-MSE


Chain C from PDB  Type:PROTEIN  Length:278
 aligned with O67636_AQUAE | O67636 from UniProtKB/TrEMBL  Length:311

    Alignment length:278
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299        
         O67636_AQUAE    30 MQNVLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKR 307
               SCOP domains d2g5cc2 C:30-200 Prephenate dehydrogenase TyrA                                                                                                                             d2g5cc1 C:201-307 Prephenate dehydrogenase TyrA                                                             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.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g5c C  30 mQNVLIVGVGFmGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVmLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYmSPELHDYVFGVVSHLPHAVAFALVDTLIHmSTPEVDLFKYPGGGFKDFTRIAKSDPImWRDIFLENKENVmKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKR 307
                            |       39 |      49        59        69        79        89      | 99       109       119       129       139       149       159       169       179       189       199|      209       219       229|      239       249       259       269 |     279       289       299        
                            |         41-MSE                                                 96-MSE                                                                                                 200-MSE                       230-MSE                     258-MSE      271-MSE                                
                           30-MSE                                                                                                                                                                                                                                                                                 


Chain D from PDB  Type:PROTEIN  Length:278
 aligned with O67636_AQUAE | O67636 from UniProtKB/TrEMBL  Length:311

    Alignment length:278
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299        
         O67636_AQUAE    30 MQNVLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKR 307
               SCOP domains d2g5cd2 D:30-200 Prephenate dehydrogenase TyrA                                                                                                                             d2g5cd1 D:201-307 Prephenate dehydrogenase TyrA                                                             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.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g5c D  30 mQNVLIVGVGFmGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVmLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYmSPELHDYVFGVVSHLPHAVAFALVDTLIHmSTPEVDLFKYPGGGFKDFTRIAKSDPImWRDIFLENKENVmKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKR 307
                            |       39 |      49        59        69        79        89      | 99       109       119       129       139       149       159       169       179       189       199|      209       219       229|      239       249       259       269 |     279       289       299        
                           30-MSE     41-MSE                                                 96-MSE                                                                                                 200-MSE                       230-MSE                     258-MSE      271-MSE
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 8)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2G5C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2G5C)

(-) 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: 3ggg 3ggo 3ggp

(-) Related Entries Specified in the PDB File

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