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(-) Description

Title :  E. COLI FRUCTOSE-1,6-BISPHOSPHATASE: CITRATE, FRU-2,6-P2, AND MG2+ BOUND
 
Authors :  J. K. Hines, H. J. Fromm, R. B. Honzatko
Date :  08 Aug 07  (Deposition) - 23 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.18
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Tetramer, Sugar Phosphatase Fold, Carbohydrate Metabolism, Cytoplasm, Hydrolase, Magnesium (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. K. Hines, X. Chen, J. C. Nix, H. J. Fromm, R. B. Honzatko
Structures Of Mammalian And Bacterial Fructose-1, 6-Bisphosphatase Reveal The Basis For Synergism In Amp/Fructose 2, 6-Bisphosphate Inhibition.
J. Biol. Chem. V. 282 36121 2007
PubMed-ID: 17933867  |  Reference-DOI: 10.1074/JBC.M707302200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FRUCTOSE-1,6-BISPHOSPHATASE
    Chains: A
    EC Number: 3.1.3.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-24B
    Expression System Strain: DF657
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FBP, FDP
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: XL1-BLUE
    Synonym: D-FRUCTOSE-1,6-BISPHOSPHATE 1-PHOSPHOHYDROLASE, FBPASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2FDP1Ligand/IonFRUCTOSE-2,6-DIPHOSPHATE
3MG1Ligand/IonMAGNESIUM ION
4MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 32)
No.NameCountTypeFull Name
1CIT4Ligand/IonCITRIC ACID
2FDP4Ligand/IonFRUCTOSE-2,6-DIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4MSE24Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:113 , GLY A:114 , SER A:115 , SER A:116 , ASN A:206 , ARG A:238 , TYR A:239 , GLY A:241 , LEU A:243 , TYR A:257 , TYR A:259 , LYS A:269 , GLU A:275 , MG A:334 , HOH A:363 , HOH A:371 , HOH A:384 , HOH A:385 , HOH A:396 , HOH A:404 , HOH A:415 , HOH A:462BINDING SITE FOR RESIDUE FDP A 333
2AC2SOFTWAREASP A:110 , ASP A:113 , GLU A:275 , FDP A:333 , HOH A:462BINDING SITE FOR RESIDUE MG A 334
3AC3SOFTWARETHR A:3 , LEU A:4 , GLY A:5 , LYS A:30 , LYS A:34 , ARG A:80 , VAL A:186 , PHE A:187 , HOH A:418BINDING SITE FOR RESIDUE CIT A 335

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg A:233 -Pro A:234

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FBPASEPS00124 Fructose-1-6-bisphosphatase active site.F16PA_ECOLI268-280  1A:268-280
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FBPASEPS00124 Fructose-1-6-bisphosphatase active site.F16PA_ECOLI268-280  4A:268-280

(-) Exons   (0, 0)

(no "Exon" information available for 2QVR)

(-) 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:332
 aligned with F16PA_ECOLI | P0A993 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:332
                                    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       280       290       300       310       320       330  
          F16PA_ECOLI     1 MKTLGEFIVEKQHEFSHATGELTALLSAIKLGAKIIHRDINKAGLVDILGASGAENVQGEVQQKLDLFANEKLKAALKARDIVAGIASEEEDEIVVFEGCEHAKYVVLMDPLDGSSNIDVNVSVGTIFSIYRRVTPVGTPVTEEDFLQPGNKQVAAGYVVYGSSTMLVYTTGCGVHAFTYDPSLGVFCLCQERMRFPEKGKTYSINEGNYIKFPNGVKKYIKFCQEEDKSTNRPYTSRYIGSLVADFHRNLLKGGIYLYPSTASHPDGKLRLLYECNPMAFLAEQAGGKASDGKERILDIIPETLHQRRSFFVGNDHMVEDVERFIREFPDA 332
               SCOP domains d2qvra_ A: automated matches                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -2qvrA01 A:2-193 Fructose-1,6-Bisphosphatase, subunit A, domain 1                                                                                                                                -2qvrA02 A:195-325  [code=3.40.190.80, no name defined]                                                                             ------- CATH domains
               Pfam domains -FBPase-2qvrA01 A:2-329                                                                                                                                                                                                                                                                                                                  --- Pfam domains
         Sec.struct. author ..hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.........eeeee.....eeehhhhhhhhhhhhhhhhh..eeeeee......ee........eeeeeeeeehhhhh.....eeeeeeeee.........hhhhh..hhhhh.eeeeeee...eeeeee....eeeeee......eeeeeeee.......eee.hhhhhhhhhhhhhhhhhhhhh.hhhhh...ee....hhhhhhhhhhhhh.eeee...............hhhhhhhhhhhh..eee....hhhhh..........eeeehhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FBPASE       ---------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qvr A   1 mKTLGEFIVEKQHEFSHATGELTALLSAIKLGAKIIHRDINKAGLVDILGASGAENVQGEVQQKLDLFANEKLKAALKARDIVAGIASEEEDEIVVFEGCEHAKYVVLmDPLDGSSNIDVNVSVGTIFSIYRRVTPVGTPVTEEDFLQPGNKQVAAGYVVYGSSTmLVYTTGCGVHAFTYDPSLGVFCLCQERmRFPEKGKTYSINEGNYIKFPNGVKKYIKFCQEEDKSTNRPYTSRYIGSLVADFHRNLLKGGIYLYPSTASHPDGKLRLLYECNPmAFLAEQAGGKASDGKERILDIIPETLHQRRSFFVGNDHmVEDVERFIREFPDA 332
                            |       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       280       290       300       310       320       330  
                            |                                                                                                         109-MSE                                                  166-MSE                     194-MSE                                                                              279-MSE                                318-MSE          
                            1-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Phospoesterase (42)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A   (F16PA_ECOLI | P0A993)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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:0016051    carbohydrate biosynthetic process    The chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
    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:0006094    gluconeogenesis    The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        F16PA_ECOLI | P0A993: 2gq1 2owz 2ox3 2q8m

(-) Related Entries Specified in the PDB File

2gq1 2owz 2ox3 2q8m 2qvu 2qvv