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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE PREPHENATE DEHYDROGENASE (CGL0226) FROM CORYNEBACTERIUM GLUTAMICUM ATCC 13032 AT 2.60 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  24 Nov 09  (Deposition) - 02 Feb 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Prephenate Dehydrogenas, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Prephenate Dehydrogenase (Np_599479. 1) From Corynebacterium Glutamicum Atcc 13032 Kitasato At 2. 60 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PREPHENATE DEHYDROGENASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CGL0226
    Organism Common: BREVIBACTERIUM FLAVUM
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM ATCC 13032
    Organism Taxid: 196627

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 26)

Asymmetric Unit (3, 26)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MSE24Mod. Amino AcidSELENOMETHIONINE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (3, 14)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MSE12Mod. Amino AcidSELENOMETHIONINE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (1, 12)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2MSE12Mod. Amino AcidSELENOMETHIONINE
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:81 , ARG A:113 , THR D:320 , ASN D:322 , TRP D:323 , GLU D:324BINDING SITE FOR RESIDUE EDO A 341
2AC2SOFTWAREGLN A:152 , LEU A:153 , ASP A:155 , THR A:157 , PHE C:340BINDING SITE FOR RESIDUE PEG A 342

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KTD)

(-) 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:323
 aligned with Q8NTS6_CORGL | Q8NTS6 from UniProtKB/TrEMBL  Length:340

    Alignment length:336
                                    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      
         Q8NTS6_CORGL     5 DISRPVCILGLGLIGGSLLRDLHAANHSVFGYNRSRSGAKSAVDEGFDVSADLEATLQRAAAEDALIVLAVPMTAIDSLLDAVHTHAPNNGFTDVVSVKTAVYDAVKARNMQHRYVGSHPMAGTANSGWSASMDGLFKRAVWVVTFDQLFDGTDINSTWISIWKDVVQMALAVGAEVVPSRVGPHDAAAARVSHLTHILAETLAIVGDNGGALSLSLAAGSYRDSTRVAGTDPGLVRAMCESNAGPLVKALDEALAILHEAREGLTAEQPNIEQLADNGYRSRIRYEARSGQRRAKESVSPTITSSRPVLRLHPGTPNWEKQLIHAETLGARIEVF 340
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee..hhhhhhhhhhhhhh...eeee..hhhhhhhhhhh...ee.hhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhh....eee....hhhhhhhhhhh.hhh.ee.eee.....-.hhhhh........eeee.hhhhh.....hhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...------------....eeee.....hhhhhhhhhhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ktd A   5 DISRPVCILGLGLIGGSLLRDLHAANHSVFGYNRSRSGAKSAVDEGFDVSADLEATLQRAAAEDALIVLAVPmTAIDSLLDAVHTHAPNNGFTDVVSVKTAVYDAVKARNmQHRYVGSHPmAGTA-SGWSASmDGLFKRAVWVVTFDQLFDGTDINSTWISIWKDVVQmALAVGAEVVPSRVGPHDAAAARVSHLTHILAETLAIVGDNGGALSLSLAAGSYRDSTRVAGTDPGLVRAmCESNAGPLVKALDEALAILHEAREGLTAEQPNIEQLADNGYRSRIRYEARSGQ------------SSRPVLRLHPGTPNWEKQLIHAETLGARIEVF 340
                                    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 |       -    |  314       324       334      
                                                                                                   77-MSE                               115-MSE   125-MSE |     |                                 173-MSE                                                               243-MSE                                              296          309                               
                                                                                                                                                        131     |                                                                                                                                                                                                           
                                                                                                                                                              137-MSE                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:319
 aligned with Q8NTS6_CORGL | Q8NTS6 from UniProtKB/TrEMBL  Length:340

    Alignment length:336
                                    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      
         Q8NTS6_CORGL     5 DISRPVCILGLGLIGGSLLRDLHAANHSVFGYNRSRSGAKSAVDEGFDVSADLEATLQRAAAEDALIVLAVPMTAIDSLLDAVHTHAPNNGFTDVVSVKTAVYDAVKARNMQHRYVGSHPMAGTANSGWSASMDGLFKRAVWVVTFDQLFDGTDINSTWISIWKDVVQMALAVGAEVVPSRVGPHDAAAARVSHLTHILAETLAIVGDNGGALSLSLAAGSYRDSTRVAGTDPGLVRAMCESNAGPLVKALDEALAILHEAREGLTAEQPNIEQLADNGYRSRIRYEARSGQRRAKESVSPTITSSRPVLRLHPGTPNWEKQLIHAETLGARIEVF 340
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee..hhhhhhhhhhhhhh...eeee..hhhhhhhhhh....ee.hhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhh........eee.......hhhhh........eeee.hhhhh.....hhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh-----------------...eeee.....hhhhhhhhhhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ktd B   5 DISRPVCILGLGLIGGSLLRDLHAANHSVFGYNRSRSGAKSAVDEGFDVSADLEATLQRAAAEDALIVLAVPmTAIDSLLDAVHTHAPNNGFTDVVSVKTAVYDAVKARNmQHRYVGSHPmAGTANSGWSASmDGLFKRAVWVVTFDQLFDGTDINSTWISIWKDVVQmALAVGAEVVPSRVGPHDAAAARVSHLTHILAETLAIVGDNGGALSLSLAAGSYRDSTRVAGTDPGLVRAmCESNAGPLVKALDEALAILHEAREGLTAEQPNIEQLADNGYRSRIRYEA-----------------SRPVLRLHPGTPNWEKQLIHAETLGARIEVF 340
                                    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       | -         -     | 314       324       334      
                                                                                                   77-MSE                               115-MSE   125-MSE     137-MSE                             173-MSE                                                               243-MSE                                          292               310                              


Chain C from PDB  Type:PROTEIN  Length:318
 aligned with Q8NTS6_CORGL | Q8NTS6 from UniProtKB/TrEMBL  Length:340

    Alignment length:336
                                    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      
         Q8NTS6_CORGL     5 DISRPVCILGLGLIGGSLLRDLHAANHSVFGYNRSRSGAKSAVDEGFDVSADLEATLQRAAAEDALIVLAVPMTAIDSLLDAVHTHAPNNGFTDVVSVKTAVYDAVKARNMQHRYVGSHPMAGTANSGWSASMDGLFKRAVWVVTFDQLFDGTDINSTWISIWKDVVQMALAVGAEVVPSRVGPHDAAAARVSHLTHILAETLAIVGDNGGALSLSLAAGSYRDSTRVAGTDPGLVRAMCESNAGPLVKALDEALAILHEAREGLTAEQPNIEQLADNGYRSRIRYEARSGQRRAKESVSPTITSSRPVLRLHPGTPNWEKQLIHAETLGARIEVF 340
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee..hhhhhhhhhhhhhh...eeee..hhhhhhhhhhh...ee.hhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhh....eee....hhhhhhhhhhh.hhhhh..eee......-hhhhh........eeee.hhhhh.....hhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.-----------------..eeee.....hhhhhhhhhhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ktd C   5 DISRPVCILGLGLIGGSLLRDLHAANHSVFGYNRSRSGAKSAVDEGFDVSADLEATLQRAAAEDALIVLAVPmTAIDSLLDAVHTHAPNNGFTDVVSVKTAVYDAVKARNmQHRYVGSHPmAGTAN-GWSASmDGLFKRAVWVVTFDQLFDGTDINSTWISIWKDVVQmALAVGAEVVPSRVGPHDAAAARVSHLTHILAETLAIVGDNGGALSLSLAAGSYRDSTRVAGTDPGLVRAmCESNAGPLVKALDEALAILHEAREGLTAEQPNIEQLADNGYRSRIRYEAR-----------------RPVLRLHPGTPNWEKQLIHAETLGARIEVF 340
                                    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        |-         -      |314       324       334      
                                                                                                   77-MSE                               115-MSE   125-MSE0 |    |                                 173-MSE                                                               243-MSE                                           293               311                             
                                                                                                                                                         132    |                                                                                                                                                                                                           
                                                                                                                                                              137-MSE                                                                                                                                                                                                       


Chain D from PDB  Type:PROTEIN  Length:321
 aligned with Q8NTS6_CORGL | Q8NTS6 from UniProtKB/TrEMBL  Length:340

    Alignment length:336
                                    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      
         Q8NTS6_CORGL     5 DISRPVCILGLGLIGGSLLRDLHAANHSVFGYNRSRSGAKSAVDEGFDVSADLEATLQRAAAEDALIVLAVPMTAIDSLLDAVHTHAPNNGFTDVVSVKTAVYDAVKARNMQHRYVGSHPMAGTANSGWSASMDGLFKRAVWVVTFDQLFDGTDINSTWISIWKDVVQMALAVGAEVVPSRVGPHDAAAARVSHLTHILAETLAIVGDNGGALSLSLAAGSYRDSTRVAGTDPGLVRAMCESNAGPLVKALDEALAILHEAREGLTAEQPNIEQLADNGYRSRIRYEARSGQRRAKESVSPTITSSRPVLRLHPGTPNWEKQLIHAETLGARIEVF 340
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ----------------PDH-3ktdD01 D:21-282                                                                                                                                                                                                                                                  ------------              -------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------PDH-3ktdD02 D:21-282                                                                                                                                                                                                                                                  ------------              -------------------------------- Pfam domains (2)
           Pfam domains (3) ----------------PDH-3ktdD03 D:21-282                                                                                                                                                                                                                                                  ------------              -------------------------------- Pfam domains (3)
           Pfam domains (4) ----------------PDH-3ktdD04 D:21-282                                                                                                                                                                                                                                                  ------------              -------------------------------- Pfam domains (4)
         Sec.struct. author .....eeee..hhhhhhhhhhhhhh...eeee..hhhhhhhhhhh...ee.hhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhhhh....eee....hhhhhhhhhhh.hhhhh..eee.....-.hhhhh........eeee.hhhhh.....hhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.--------------....eeee.......hhhhhhhhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ktd D   5 DISRPVCILGLGLIGGSLLRDLHAANHSVFGYNRSRSGAKSAVDEGFDVSADLEATLQRAAAEDALIVLAVPmTAIDSLLDAVHTHAPNNGFTDVVSVKTAVYDAVKARNmQHRYVGSHPmAGTA-SGWSASmDGLFKRAVWVVTFDQLFDGTDINSTWISIWKDVVQmALAVGAEVVPSRVGPHDAAAARVSHLTHILAETLAIVGDNGGALSLSLAAGSYRDSTRVAGTDPGLVRAmCESNAGPLVKALDEALAILHEAREGLTAEQPNIEQLADNGYRSRIRYEARS--------------SSRPVLRLHPGTPNWEKQLIHAETLGARIEVF 340
                                    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         -    |  314       324       334      
                                                                                                   77-MSE                               115-MSE   125-MSE |     |                                 173-MSE                                                               243-MSE                                            294            309                               
                                                                                                                                                        131     |                                                                                                                                                                                                           
                                                                                                                                                              137-MSE
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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  (0, 0)

(no "SCOP Domain" information available for 3KTD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8NTS6_CORGL | Q8NTS6)
molecular function
    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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