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(-) Description

Title :  R-STATE AMP COMPLEX REVEALS INITIAL STEPS OF THE QUATERNARY TRANSITION OF FRUCTOSE-1,6-BISPHOSPHATASE
 
Authors :  C. V. Iancu, S. Mukund, H. J. Fromm, R. B. Honzatko
Date :  25 Feb 05  (Deposition) - 15 Mar 05  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Allostearic Enzymes, Intermediate States, Fructose-1, 6- Bisphosphatase, Fbpase, Glycolysis, Gluconeogenesis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. V. Iancu, S. Mukund, H. J. Fromm, R. B. Honzatko
R-State Amp Complex Reveals Initial Steps Of The Quaternary Transition Of Fructose-1, 6-Bisphosphatase.
J. Biol. Chem. V. 280 19737 2005
PubMed-ID: 15767255  |  Reference-DOI: 10.1074/JBC.M501011200

(-) Compounds

Molecule 1 - FRUCTOSE-1,6-BISPHOSPHATASE
    ChainsA
    EC Number3.1.3.11
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainDF 657
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneFBP1, FBP
    MutationYES
    Organism CommonPIG
    Organism ScientificSUS SCROFA
    Organism Taxid9823
    Other DetailsR-STATE
    SynonymD-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, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2F6P1Ligand/IonFRUCTOSE-6-PHOSPHATE
3MG2Ligand/IonMAGNESIUM ION
4PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1AMP4Ligand/IonADENOSINE MONOPHOSPHATE
2F6P4Ligand/IonFRUCTOSE-6-PHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4PO44Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:121 , GLY A:122 , ASN A:212 , TYR A:215 , ARG A:243 , TYR A:244 , GLY A:246 , SER A:247 , MET A:248 , TYR A:264 , LYS A:274 , ARG A:276 , MG A:341 , PO4 A:434 , HOH A:523 , HOH A:541 , HOH A:546 , HOH A:561 , HOH A:653BINDING SITE FOR RESIDUE F6P A 339
2AC2SOFTWAREGLU A:97 , ASP A:118 , LEU A:120 , ASP A:121 , GLY A:122 , SER A:123 , ARG A:276 , GLU A:280 , F6P A:339 , MG A:340 , MG A:341 , HOH A:647 , HOH A:660BINDING SITE FOR RESIDUE PO4 A 434
3AC3SOFTWAREGLU A:97 , ASP A:118 , LEU A:120 , PO4 A:434BINDING SITE FOR RESIDUE MG A 340
4AC4SOFTWAREASP A:118 , ASP A:121 , GLU A:280 , F6P A:339 , PO4 A:434BINDING SITE FOR RESIDUE MG A 341
5AC5SOFTWAREVAL A:17 , GLU A:20 , GLY A:21 , ALA A:24 , THR A:27 , GLY A:28 , GLU A:29 , MET A:30 , THR A:31 , LYS A:112 , TYR A:113 , ARG A:140 , MET A:177 , HOH A:710 , HOH A:716BINDING SITE FOR RESIDUE AMP A 435

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YYZ)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FBPASEPS00124 Fructose-1-6-bisphosphatase active site.F16P1_PIG274-286  1A:273-285
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FBPASEPS00124 Fructose-1-6-bisphosphatase active site.F16P1_PIG274-286  4A:273-285

(-) Exons   (0, 0)

(no "Exon" information available for 1YYZ)

(-) 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:326
 aligned with F16P1_PIG | P00636 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:326
                                    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      
            F16P1_PIG    11 IVTLTRFVMEEGRKARGTGEMTQLLNSLCTAVKAISTAVRKAGIAHLYGIAGSTNVTGDQVKKLDVLSNDLVINVLKSSFATCVLVSEEDKNAIIVEPEKRGKYVVCFDPLDGSSNIDCLVSIGTIFGIYRKNSTDEPSEKDALQPGRNLVAAGYALYGSATMLVLAMVNGVNCFMLDPAIGEFILVDRDVKIKKKGSIYSINEGYAKEFDPAITEYIQRKKFPPDNSAPYGARYVGSMVADVHRTLVYGGIFMYPANKKSPKGKLRLLYECNPMAYVMEKAGGLATTGKEAVLDIVPTDIHQRAPIILGSPEDVTELLEIYQKHA 336
               SCOP domains d1yyza_ A: Fructose-1,6-bisphosphatase                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1yyzA01 A:10-199 Fructose-1,6-Bisphosphatase, subunit A, domain 1                                                                                                                             1yyzA02 A:200-334  [code=3.40.190.80, no name defined]                                                                                 - CATH domains
               Pfam domains -FBPase-1yyzA01 A:11-334                                                                                                                                                                                                                                                                                                             - Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.........eeeee.....eeehhhhhhhhhhhhhhhhh..eeeeee......ee.....eeeeeeeeeeeehhhhh.....eeeeeeeee.......hhhhhh.hhhhh.eeeeeee...eeeeeee..eeeeeeee....eeeeee..........eee.hhhhh...hhhhhhhhhhhhh........ee....hhhhhhhhhhhhh.eeee...............hhhhhhhhhhhh..eee....hhhhh..........eeeehhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FBPASE       -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yyz A  10 IVTLTRFVMEEGRKARGTGEMTQLLNSLCTAVKAISTAVRKAGILHLYGIAGSTNVTGDQVKKLDVLSNDLVINVLKSSFATCVLVSEEDKNAIIVEPEKRGKYVVCFDPLDGSSNIDCLVSIGTIFGIYRKNSTDEPSEKDALQPGRNLVAAGYALYGSATMLVLAMVNGVNCFMLDPAIGEFILVDRDVKIKKKGSIYSINEGYAKEFDPAITEYIQRKKFPPDNSAPYGARYVGSMVADVHRTLVYGGIFMYPANKKSPKGKLRLLYECNPMAYVMEKAGGLATTGKEAVLDIVPTDIHQRAPIILGSPEDVTELLEIYQKHA 335
                                    19        29        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       319       329      

   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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A   (F16P1_PIG | P00636)
molecular function
    GO:0016208    AMP binding    Interacting selectively and non-covalently with AMP, adenosine monophosphate.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0048029    monosaccharide binding    Interacting selectively and non-covalently with any monosaccharide. Monosaccharides are the simplest carbohydrates; they are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H[CHOH]nC(=O)[CHOH]mH with three or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
    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:0035690    cellular response to drug    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0071286    cellular response to magnesium ion    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a magnesium ion stimulus.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0006002    fructose 6-phosphate metabolic process    The chemical reactions and pathways involving fructose 6-phosphate, also known as F6P. The D-enantiomer is an important intermediate in glycolysis, gluconeogenesis, and fructose metabolism.
    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:0046580    negative regulation of Ras protein signal transduction    Any process that stops, prevents, or reduces the frequency, rate or extent of Ras protein signal transduction.
    GO:0030308    negative regulation of cell growth    Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
    GO:0045820    negative regulation of glycolytic process    Any process that stops, prevents, or reduces the frequency, rate or extent of glycolysis.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0006111    regulation of gluconeogenesis    Any process that modulates the frequency, rate or extent of gluconeogenesis, the formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
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
        F16P1_PIG | P006361cnq 1eyi 1eyj 1eyk 1fbc 1fbd 1fbe 1fbf 1fbg 1fbh 1fbp 1fj6 1fj9 1fpb 1fpd 1fpe 1fpf 1fpg 1fpi 1fpj 1fpk 1fpl 1frp 1fsa 1kz8 1lev 1nuw 1nux 1nuy 1nuz 1nv0 1nv1 1nv2 1nv3 1nv4 1nv5 1nv6 1nv7 1q9d 1rdx 1rdy 1rdz 1yxi 1yz0 2f3b 2f3d 2fbp 2qvu 2qvv 3fbp 4fbp 4gbv 4gbw 4gws 4gwu 4gww 4gwx 4gwy 4gwz 4gx3 4gx4 4gx6 4h45 4h46 4kxp 5fbp

(-) Related Entries Specified in the PDB File

1cnq
1fj6
1nuy
1yxi A54L, R-STATE
1yz0 A54L, T-STATE COMPLEX