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(-) Description

Title :  CRYSTAL STRUCTURE OF SYNECHOCYSTIS AROGENATE DEHYDROGENASE
 
Authors :  P. Legrand, R. Dumas, M. Seux, P. Rippert, R. Ravelli, J. -L. Ferrer, M. M
Date :  14 Nov 05  (Deposition) - 09 May 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Arogenate/Prephenate Dehydrogenase, Tyrosine Synthesis, X-Ray Crystallography Structure, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Legrand, R. Dumas, M. Seux, P. Rippert, R. Ravelli, J. -L. Ferrer, M. Matringe
Biochemical Characterization And Crystal Structure Of Synechocystis Arogenate Dehydrogenase Provide Insights Into Catalytic Reaction
Structure V. 14 767 2006
PubMed-ID: 16615917  |  Reference-DOI: 10.1016/J.STR.2006.01.006

(-) Compounds

Molecule 1 - PREPHENATE DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.3.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29
    Expression System Strain: BL21 (LAMBDA DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: D90910.1
    Organism Scientific: SYNECHOCYSTIS SP.
    Organism Taxid: 1148
    Strain: PCC 6803
    Synonym: AROGENATE DEHYDROGENASE

 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  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2OCS4Mod. Amino AcidCYSTEINESULFONIC ACID
3OMT4Mod. Amino AcidS-DIOXYMETHIONINE
4TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2OCS2Mod. Amino AcidCYSTEINESULFONIC ACID
3OMT2Mod. Amino AcidS-DIOXYMETHIONINE
4TRS-1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (4, 8)
No.NameCountTypeFull Name
1NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2OCS2Mod. Amino AcidCYSTEINESULFONIC ACID
3OMT2Mod. Amino AcidS-DIOXYMETHIONINE
4TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP C:197 , ASP C:199 , ASP D:169 , HOH D:4423BINDING SITE FOR RESIDUE TRS C 1001
2AC2SOFTWAREGLU B:126 , GLU B:127 , ASN B:128 , LEU B:129 , GLU D:126 , GLU D:127 , ASN D:128 , LEU D:129 , HOH D:4417 , HOH D:4424BINDING SITE FOR RESIDUE TRS D 1002
3AC3SOFTWAREGLY A:7 , GLY A:9 , LEU A:10 , ILE A:11 , SER A:30 , ARG A:31 , GLN A:32 , THR A:35 , CYS A:64 , THR A:65 , PRO A:66 , ILE A:67 , VAL A:90 , ALA A:91 , SER A:92 , PRO A:113 , ALA A:115 , GLY A:116 , THR A:117 , GLN A:120 , GLY A:121 , HOH A:1352 , HOH A:1370 , HOH A:1392BINDING SITE FOR RESIDUE NAP A 1350
4AC4SOFTWAREGLY B:7 , GLY B:9 , LEU B:10 , ILE B:11 , SER B:30 , ARG B:31 , GLN B:32 , THR B:35 , CYS B:64 , THR B:65 , PRO B:66 , ILE B:67 , LEU B:69 , VAL B:90 , ALA B:91 , SER B:92 , PRO B:113 , ALA B:115 , GLN B:120 , GLY B:121 , HOH B:2355 , HOH B:2395 , HOH B:2450BINDING SITE FOR RESIDUE NAP B 2350
5AC5SOFTWAREGLY C:7 , GLY C:9 , LEU C:10 , ILE C:11 , SER C:30 , ARG C:31 , GLN C:32 , THR C:35 , CYS C:64 , THR C:65 , ILE C:67 , LEU C:69 , VAL C:90 , ALA C:91 , SER C:92 , HIS C:112 , PRO C:113 , ALA C:115 , GLY C:116 , GLN C:120 , GLY C:121BINDING SITE FOR RESIDUE NAP C 3350
6AC6SOFTWAREGLY D:7 , GLY D:9 , LEU D:10 , ILE D:11 , SER D:30 , ARG D:31 , GLN D:32 , THR D:35 , CYS D:64 , THR D:65 , PRO D:66 , ILE D:67 , LEU D:69 , VAL D:90 , ALA D:91 , SER D:92 , HIS D:112 , PRO D:113 , ALA D:115 , GLY D:116 , GLN D:120 , GLY D:121 , HOH D:4355 , HOH D:4369 , HOH D:4401 , HOH D:4430 , HOH D:4470 , HOH D:4474BINDING SITE FOR RESIDUE NAP D 4350

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F1K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2F1K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F1K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2F1K)

(-) Exons   (0, 0)

(no "Exon" information available for 2F1K)

(-) 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:279
 aligned with P73906_SYNY3 | P73906 from UniProtKB/TrEMBL  Length:279

    Alignment length:279
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270         
         P73906_SYNY3     1 MKIGVVGLGLIGASLAGDLRRRGHYLIGVSRQQSTCEKAVERQLVDEAGQDLSLLQTAKIIFLCTPIQLILPTLEKLIPHLSPTAIVTDVASVKTAIAEPASQLWSGFIGGHPMAGTAAQGIDGAEENLFVNAPYVLTPTEYTDPEQLACLRSVLEPLGVKIYLCTPADHDQAVAWISHLPVMVSAALIQACAGEKDGDILKLAQNLASSGFRDTSRVGGGNPELGTMMATYNQRALLKSLQDYRQHLDQLITLISNQQWPELHRLLQQTNGDRDKYVE 279
               SCOP domains d2f1ka2 A:1-165 Prephenate dehydrogenase TyrA                                                                                                                        d2f1ka1 A:166-279 Prephenate dehydrogenase TyrA                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh....eee.hhhhhh...eeee..hhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhh...eeeee.......hhhhh........eeeeee....hhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f1k A   1 MKIGVVGLGLIGASLAGDLRRRGHYLIGVSRQQSTCEKAVERQLVDEAGQDLSLLQTAKIIFLCTPIQLILPTLEKLIPHLSPTAIVTDVASVKTAIAEPASQLWSGFIGGHPmAGTAAQGIDGAEENLFVNAPYVLTPTEYTDPEQLAcLRSVLEPLGVKIYLCTPADHDQAVAWISHLPVMVSAALIQACAGEKDGDILKLAQNLASSGFRDTSRVGGGNPELGTMMATYNQRALLKSLQDYRQHLDQLITLISNQQWPELHRLLQQTNGDRDKYVE 279
                                    10        20        30        40        50        60        70        80        90       100       110   |   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270         
                                                                                                                                           114-OMT                             150-OCS                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:279
 aligned with P73906_SYNY3 | P73906 from UniProtKB/TrEMBL  Length:279

    Alignment length:279
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270         
         P73906_SYNY3     1 MKIGVVGLGLIGASLAGDLRRRGHYLIGVSRQQSTCEKAVERQLVDEAGQDLSLLQTAKIIFLCTPIQLILPTLEKLIPHLSPTAIVTDVASVKTAIAEPASQLWSGFIGGHPMAGTAAQGIDGAEENLFVNAPYVLTPTEYTDPEQLACLRSVLEPLGVKIYLCTPADHDQAVAWISHLPVMVSAALIQACAGEKDGDILKLAQNLASSGFRDTSRVGGGNPELGTMMATYNQRALLKSLQDYRQHLDQLITLISNQQWPELHRLLQQTNGDRDKYVE 279
               SCOP domains d2f1kb2 B:1-165 Prephenate dehydrogenase TyrA                                                                                                                        d2f1kb1 B:166-279 Prephenate dehydrogenase TyrA                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh....eee.hhhhhh...eeee..hhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhh..eeeeee.......hhhhh........eeeee.....hhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f1k B   1 MKIGVVGLGLIGASLAGDLRRRGHYLIGVSRQQSTCEKAVERQLVDEAGQDLSLLQTAKIIFLCTPIQLILPTLEKLIPHLSPTAIVTDVASVKTAIAEPASQLWSGFIGGHPmAGTAAQGIDGAEENLFVNAPYVLTPTEYTDPEQLAcLRSVLEPLGVKIYLCTPADHDQAVAWISHLPVMVSAALIQACAGEKDGDILKLAQNLASSGFRDTSRVGGGNPELGTMMATYNQRALLKSLQDYRQHLDQLITLISNQQWPELHRLLQQTNGDRDKYVE 279
                                    10        20        30        40        50        60        70        80        90       100       110   |   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270         
                                                                                                                                           114-OMT                             150-OCS                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:278
 aligned with P73906_SYNY3 | P73906 from UniProtKB/TrEMBL  Length:279

    Alignment length:278
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270        
         P73906_SYNY3     1 MKIGVVGLGLIGASLAGDLRRRGHYLIGVSRQQSTCEKAVERQLVDEAGQDLSLLQTAKIIFLCTPIQLILPTLEKLIPHLSPTAIVTDVASVKTAIAEPASQLWSGFIGGHPMAGTAAQGIDGAEENLFVNAPYVLTPTEYTDPEQLACLRSVLEPLGVKIYLCTPADHDQAVAWISHLPVMVSAALIQACAGEKDGDILKLAQNLASSGFRDTSRVGGGNPELGTMMATYNQRALLKSLQDYRQHLDQLITLISNQQWPELHRLLQQTNGDRDKYV 278
               SCOP domains d2f1kc2 C:1-165 Prephenate dehydrogenase TyrA                                                                                                                        d2f1kc1 C:166-278 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..eeeeee.......hhhhh........eeeee.....hhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f1k C   1 MKIGVVGLGLIGASLAGDLRRRGHYLIGVSRQQSTCEKAVERQLVDEAGQDLSLLQTAKIIFLCTPIQLILPTLEKLIPHLSPTAIVTDVASVKTAIAEPASQLWSGFIGGHPmAGTAAQGIDGAEENLFVNAPYVLTPTEYTDPEQLAcLRSVLEPLGVKIYLCTPADHDQAVAWISHLPVMVSAALIQACAGEKDGDILKLAQNLASSGFRDTSRVGGGNPELGTMMATYNQRALLKSLQDYRQHLDQLITLISNQQWPELHRLLQQTNGDRDKYV 278
                                    10        20        30        40        50        60        70        80        90       100       110   |   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270        
                                                                                                                                           114-OMT                             150-OCS                                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:279
 aligned with P73906_SYNY3 | P73906 from UniProtKB/TrEMBL  Length:279

    Alignment length:279
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270         
         P73906_SYNY3     1 MKIGVVGLGLIGASLAGDLRRRGHYLIGVSRQQSTCEKAVERQLVDEAGQDLSLLQTAKIIFLCTPIQLILPTLEKLIPHLSPTAIVTDVASVKTAIAEPASQLWSGFIGGHPMAGTAAQGIDGAEENLFVNAPYVLTPTEYTDPEQLACLRSVLEPLGVKIYLCTPADHDQAVAWISHLPVMVSAALIQACAGEKDGDILKLAQNLASSGFRDTSRVGGGNPELGTMMATYNQRALLKSLQDYRQHLDQLITLISNQQWPELHRLLQQTNGDRDKYVE 279
               SCOP domains d2f1kd2 D:1-165 Prephenate dehydrogenase TyrA                                                                                                                        d2f1kd1 D:166-279 Prephenate dehydrogenase TyrA                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh....eee.hhhhhh...eeee..hhhhhhhhhhhhhhhh....eeee.......hhhhhhhhh..eeeeee.......hhhhh........eeeee.....hhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f1k D   1 MKIGVVGLGLIGASLAGDLRRRGHYLIGVSRQQSTCEKAVERQLVDEAGQDLSLLQTAKIIFLCTPIQLILPTLEKLIPHLSPTAIVTDVASVKTAIAEPASQLWSGFIGGHPmAGTAAQGIDGAEENLFVNAPYVLTPTEYTDPEQLAcLRSVLEPLGVKIYLCTPADHDQAVAWISHLPVMVSAALIQACAGEKDGDILKLAQNLASSGFRDTSRVGGGNPELGTMMATYNQRALLKSLQDYRQHLDQLITLISNQQWPELHRLLQQTNGDRDKYVE 279
                                    10        20        30        40        50        60        70        80        90       100       110   |   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270         
                                                                                                                                           114-OMT                             150-OCS
   Legend:   → Mismatch (orange background)
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  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  (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 2F1K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F1K)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (P73906_SYNY3 | P73906)
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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