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(-) Description

Title :  REDOX SIGNALING IN THE CHLOROPLAST: STRUCTURE OF OXIDIZED PEA FRUCTOSE-1,6-BISPHOSPHATE PHOSPHATASE
 
Authors :  M. Chiadmi, A. Navaza, M. Miginiac-Maslow, J. P. Jacquot, J. Cherfils
Date :  05 Nov 99  (Deposition) - 03 Dec 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Chloroplast, Photosynthesis, Redox Regulation, Thioredoxin, Allostery, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Chiadmi, A. Navaza, M. Miginiac-Maslow, J. P. Jacquot, J. Cherfils
Redox Signalling In The Chloroplast: Structure Of Oxidized Pea Fructose-1, 6-Bisphosphate Phosphatase.
Embo J. V. 18 6809 1999
PubMed-ID: 10581254  |  Reference-DOI: 10.1093/EMBOJ/18.23.6809
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FRUCTOSE-1,6-BISPHOSPHATASE
    Chains: A, B, C, D
    EC Number: 3.1.3.11
    Mutation: YES
    Organelle: CHLOROPLAST
    Organism Common: PEA
    Organism Scientific: PISUM SATIVUM
    Organism Taxid: 3888

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1DCU)

(-) Sites  (0, 0)

(no "Site" information available for 1DCU)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:153 -A:173
2B:153 -B:173
3C:153 -C:173
4D:153 -D:173

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1DCU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DCU)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FBPASEPS00124 Fructose-1-6-bisphosphatase active site.F16P1_PEA348-360
 
 
 		  4A:298-310
B:298-310
C:298-310
D:298-310

(-) Exons   (0, 0)

(no "Exon" information available for 1DCU)

(-) Sequences/Alignments

Asymmetric/Biological 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:330
 aligned with F16P1_PEA | P46275 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:346
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401      
            F16P1_PEA    62 KRSGYEIITLTSWLLQQEQKGIIDAELTIVLSSISMACKQIASLVQRANISNLTGTQGAVNIQGEDQKKLDVISNEVFSNCLRSSGRTGIIASEEEDVAVAVEESYSGNYIVVFDPLDGSSNLDAAVSTGSIFGIYSPNDECLPDFGDDSDDNTLGTEEQRCIVNVCQPGSNLLAAGYCMYSSSVAFVLTIGKGVFVFTLDPLYGEFVLTQENLQIPKSGEIYSFNEGNYKLWDENLKKYIDDLKEPGPSGKPYSARYIGSLVGDFHRTLLYGGIYGYPRDKKSKNGKLRLLYECAPMSFIVEQAGGKGSDGHQRVLDIQPTEIHQRVPLYIGSTEEVEKVEKYLA 407
               SCOP domains d1dcua_ A: Fructose-1,6-bisphosphatase                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---1dcuA01 A:15-224 Fructose-1,6-Bisphosphatase, subunit         A, domain 1                                                                                                                                         1dcuA02 A:225-355  [code=3.40.190.80, no name defined]                                                                             -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....--------hhhhhhhhhhhhhhhhhh...eeeeee........eeeeee.....eeeee......hhhhh..eeeeeeee........--------...hhhhhhhhhhhh.....eeeeeeeee...eeeeee....eeeeeee....eeeeee..........eee.hhhhhhhhhhhhhhhhhhhhh........ee....hhhhhhhhhhhhh.eeee...............hhhhhhhhhhhh..eee.....hhhh..........eeeehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FBPASE       ----------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dcu A  12 KRSGYEIITLTSWLLQQEQKGIIDAELTIVLSSISMACKQIASLVQRANISNLTGT--------EDQKKLDVISNEVFSNCLRSSGRTGIIASEEEDVPVAVEESYSGNYIVVFDPLDGSSNLDAAVSTGSIFGIYSPNDECLP--------NTLGTEEQRCIVNVCQPGSNLLAAGYCMYSSSVIFVLTIGKGVFVFTLDPLYGEFVLTQENLQIPKSGKIYSFNEGNYKLWDENLKKYIDDLKEPGPSGKPYSARYIGSLVGDFHRTLLYGGIYGYPRDKKSKNGKLRLLYECAPMSFIVEQAGGKGSDGHQRVLDIQPTEIHQRVPLYIGSTEEVEKVEKYLA 357
                                    21        31        41        51        61     |   -    |   81        91       101       111       121       131       141       151   |     -  |    171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351      
                                                                                  67       76                                                                            155      164                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:323
 aligned with F16P1_PEA | P46275 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:341
                                    76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406 
            F16P1_PEA    67 EIITLTSWLLQQEQKGIIDAELTIVLSSISMACKQIASLVQRANISNLTGTQGAVNIQGEDQKKLDVISNEVFSNCLRSSGRTGIIASEEEDVAVAVEESYSGNYIVVFDPLDGSSNLDAAVSTGSIFGIYSPNDECLPDFGDDSDDNTLGTEEQRCIVNVCQPGSNLLAAGYCMYSSSVAFVLTIGKGVFVFTLDPLYGEFVLTQENLQIPKSGEIYSFNEGNYKLWDENLKKYIDDLKEPGPSGKPYSARYIGSLVGDFHRTLLYGGIYGYPRDKKSKNGKLRLLYECAPMSFIVEQAGGKGSDGHQRVLDIQPTEIHQRVPLYIGSTEEVEKVEKYLA 407
               SCOP domains d1dcub_ B: Fructose-1,6-bisphosphatase                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1dcuB01 B:17-224 Fructose-1,6-Bisphosphatase, su           bunit A, domain 1                                                                                                                                    1dcuB02 B:225-355  [code=3.40.190.80, no name defined]                                                                             -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.-----------.hhhhhhhhhhhhhhhhhh..eeeeee........eeeeee.....eeeee.............eeeeeeee........-------....hhhhhhhhhhhh.....eeeeeeeee...eeeeee.....eeeeee....eeeeee..........eee.hhhhhhhhhhhhhhhhhhhh.........ee....hhhhhhhhhhhhh.eeee...............hhhhhhhhhhhh..eee.....hhhh..........eeeehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FBPASE       ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dcu B  17 EIITLTSWLLQQEQKGIIDAELTIVLSSISMACKQIASLVQRANISNL-----------EDQKKLDVISNEVFSNCLRSSGRTGIIASEEEDVPVAVEESYSGNYIVVFDPLDGSSNLDAAVSTGSIFGIYSPNDECLP-------DNTLGTEEQRCIVNVCQPGSNLLAAGYCMYSSSVIFVLTIGKGVFVFTLDPLYGEFVLTQENLQIPKSGKIYSFNEGNYKLWDENLKKYIDDLKEPGPSGKPYSARYIGSLVGDFHRTLLYGGIYGYPRDKKSKNGKLRLLYECAPMSFIVEQAGGKGSDGHQRVLDIQPTEIHQRVPLYIGSTEEVEKVEKYLA 357
                                    26        36        46        56       | -        76        86        96       106       116       126       136       146        |-      |166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356 
                                                                          64          76                                                                            155     163                                                                                                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:328
 aligned with F16P1_PEA | P46275 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:342
                                    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405  
            F16P1_PEA    66 YEIITLTSWLLQQEQKGIIDAELTIVLSSISMACKQIASLVQRANISNLTGTQGAVNIQGEDQKKLDVISNEVFSNCLRSSGRTGIIASEEEDVAVAVEESYSGNYIVVFDPLDGSSNLDAAVSTGSIFGIYSPNDECLPDFGDDSDDNTLGTEEQRCIVNVCQPGSNLLAAGYCMYSSSVAFVLTIGKGVFVFTLDPLYGEFVLTQENLQIPKSGEIYSFNEGNYKLWDENLKKYIDDLKEPGPSGKPYSARYIGSLVGDFHRTLLYGGIYGYPRDKKSKNGKLRLLYECAPMSFIVEQAGGKGSDGHQRVLDIQPTEIHQRVPLYIGSTEEVEKVEKYLA 407
               SCOP domains d1dcuc_ C: Fructose-1,6-bisphosphatase                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1dcuC01 C:16-224 Fructose-1,6-Bisphosphatase, subu          nit A, domain 1                                                                                                                                      1dcuC02 C:225-355  [code=3.40.190.80, no name defined]                                                                             -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh----------.hhhhhhhhhhhhhhhhh...eeeeee........eeeeee.....eeeee.............eeeeeeee..........----.....hhhhhhhhhhhh.....eeeeeeeee...eeeeee....eeeeeee....eeeeee..........eee.hhhhhhhhhhhhhhhhhhhh.........ee....hhhhhhhhhhhhh.eeee...............hhhhhhhhhhhh..eee.....hhhh..........eeeehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FBPASE       ----------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1dcu C  16 YEIITLTSWLLQQEQKGIIDAELTIVLSSISMACKQIASLVQRANISNLT----------EDQKKLDVISNEVFSNCLRSSGRTGIIASEEEDVPVAVEESYSGNYIVVFDPLDGSSNLDAAVSTGSIFGIYSPNDECLPDF----DDNTLGTEEQRCIVNVCQPGSNLLAAGYCMYSSSVIFVLTIGKGVFVFTLDPLYGEFVLTQENLQIPKSGKIYSFNEGNYKLWDENLKKYIDDLKEPGPSGKPYSARYIGSLVGDFHRTLLYGGIYGYPRDKKSKNGKLRLLYECAPMSFIVEQAGGKGSDGHQRVLDIQPTEIHQRVPLYIGSTEEVEKVEKYLA 357
                                    25        35        45        55        65         -|       85        95       105       115       125       135       145       155 |    |165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355  
                                                                            65         76                                                                              157  162                                                                                                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:325
 aligned with F16P1_PEA | P46275 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:341
                                    76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406 
            F16P1_PEA    67 EIITLTSWLLQQEQKGIIDAELTIVLSSISMACKQIASLVQRANISNLTGTQGAVNIQGEDQKKLDVISNEVFSNCLRSSGRTGIIASEEEDVAVAVEESYSGNYIVVFDPLDGSSNLDAAVSTGSIFGIYSPNDECLPDFGDDSDDNTLGTEEQRCIVNVCQPGSNLLAAGYCMYSSSVAFVLTIGKGVFVFTLDPLYGEFVLTQENLQIPKSGEIYSFNEGNYKLWDENLKKYIDDLKEPGPSGKPYSARYIGSLVGDFHRTLLYGGIYGYPRDKKSKNGKLRLLYECAPMSFIVEQAGGKGSDGHQRVLDIQPTEIHQRVPLYIGSTEEVEKVEKYLA 407
               SCOP domains d1dcud_ D: Fructose-1,6-bisphosphatase                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1dcuD01 D:17-224 Fructose-1,6-Bisphosphatase, subu         nit A, domain 1                                                                                                                                      1dcuD02 D:225-355  [code=3.40.190.80, no name defined]                                                                             -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...---------.hhhhhhhhhhhhhhhhhh..eeeeee........eeeeee.....eeeee......hhhhh..eeeeeeee........-------....hhhhhhhhhhhh.....eeeeeeeee...eeeeee....eeeeeee....eeeeeeeee.......eee.hhhhhhhhhhhhhhhhhhhh.........ee....hhhhhhhhhhhhh.eeee...............hhhhhhhhhhhh..eee.....hhhh..........eeeehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FBPASE       ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dcu D  17 EIITLTSWLLQQEQKGIIDAELTIVLSSISMACKQIASLVQRANISNLTG---------EDQKKLDVISNEVFSNCLRSSGRTGIIASEEEDVPVAVEESYSGNYIVVFDPLDGSSNLDAAVSTGSIFGIYSPNDECLP-------DNTLGTEEQRCIVNVCQPGSNLLAAGYCMYSSSVIFVLTIGKGVFVFTLDPLYGEFVLTQENLQIPKSGKIYSFNEGNYKLWDENLKKYIDDLKEPGPSGKPYSARYIGSLVGDFHRTLLYGGIYGYPRDKKSKNGKLRLLYECAPMSFIVEQAGGKGSDGHQRVLDIQPTEIHQRVPLYIGSTEEVEKVEKYLA 357
                                    26        36        46        56        66        76        86        96       106       116       126       136       146        |-      |166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356 
                                                                            66        76                                                                            155     163
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DCU)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (F16P1_PEA | P46275)
molecular function
    GO:0042132    fructose 1,6-bisphosphate 1-phosphatase activity    Catalysis of the reaction: D-fructose 1,6-bisphosphate + H2O = D-fructose 6-phosphate + phosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0042578    phosphoric ester hydrolase activity    Catalysis of the reaction: RPO-R' + H2O = RPOOH + R'H. This reaction is the hydrolysis of any phosphoric ester bond, any ester formed from orthophosphoric acid, O=P(OH)3.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0019253    reductive pentose-phosphate cycle    The fixation of carbon dioxide (CO2) as glucose in the chloroplasts of C3 plants; uses ATP and NADPH formed in the light reactions of photosynthesis; carbon dioxide reacts with ribulose 1,5-bisphosphate (catalyzed by the function of ribulose-bisphosphate carboxylase) to yield two molecules of 3-phosphoglycerate; these are then phosphorylated by ATP to 1,3-bisphosphateglyceraldehyde which, in turn, is then reduced by NADPH to glyceraldehyde 3-phosphate. The glyceraldehyde 3-phosphate is converted to fructose 5-phosphate and ribulose 5-phosphate by aldolase and other enzymes; the ribulose 5-phosphate is phosphorylated by ATP to ribulose 1,5-bisphosphate.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009570    chloroplast stroma    The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        F16P1_PEA | P46275: 1d9q 1dbz

(-) Related Entries Specified in the PDB File

1d9q 1D9Q CONTAINS ANOTHER CRYSTAL FORM OF THE SAME WILD TYPE PROTEIN
1dbz CRYSTAL STRUCTURE OF THE C153S MUTANT OF PEA FRUCTOSE-1,6- BISPHOSPHATASE