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(-) Description

Title :  FRUCTOSE-1,6-BISPHOSPHATASE COMPLEX WITH AMP, MAGNESIUM, FRUCTOSE-6-PHOSPHATE, PHOSPHATE AND THALLIUM (20 MM)
 
Authors :  J. Choe, C. V. Iancu, H. J. Fromm, R. B. Honzatko
Date :  02 Feb 03  (Deposition) - 08 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Bisphosphatase, Allosteric Enzymes, Gluconeogenesis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Y. Choe, S. W. Nelson, H. J. Fromm, R. B. Honzatko
Interaction Of Tl+ With Product Complexes Of Fructose-1, 6-Bisphosphatase
J. Biol. Chem. V. 278 16008 2003
PubMed-ID: 12595529  |  Reference-DOI: 10.1074/JBC.M212394200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FRUCTOSE-1,6-BISPHOSPHATASE
    ChainsA, B
    EC Number3.1.3.11
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonPIG
    Organism ScientificSUS SCROFA
    Organism Taxid9823

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)AB
Biological Unit 2 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 16)

Asymmetric Unit (5, 16)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2F6P2Ligand/IonFRUCTOSE-6-PHOSPHATE
3MG2Ligand/IonMAGNESIUM ION
4PO42Ligand/IonPHOSPHATE ION
5TL8Ligand/IonTHALLIUM (I) ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2F6P2Ligand/IonFRUCTOSE-6-PHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4PO42Ligand/IonPHOSPHATE ION
5TL-1Ligand/IonTHALLIUM (I) ION
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
1AMP4Ligand/IonADENOSINE MONOPHOSPHATE
2F6P4Ligand/IonFRUCTOSE-6-PHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4PO44Ligand/IonPHOSPHATE ION
5TL-1Ligand/IonTHALLIUM (I) ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:1121 , GLY A:1122 , ASN A:1212 , TYR A:1215 , TYR A:1244 , GLY A:1246 , SER A:1247 , MET A:1248 , TYR A:1264 , LYS A:1274 , GLU A:1280 , TL A:3351 , PO4 A:3434 , HOH A:5027 , HOH A:5045 , HOH A:5112 , HOH A:5144 , HOH A:5257 , ARG B:2243BINDING SITE FOR RESIDUE F6P A 3336
02AC2SOFTWAREARG A:1243 , ASP B:2121 , GLY B:2122 , ASN B:2212 , TYR B:2215 , TYR B:2244 , GLY B:2246 , SER B:2247 , MET B:2248 , TYR B:2264 , LYS B:2274 , GLU B:2280 , MG B:4341 , TL B:4351 , PO4 B:4434 , HOH B:5014 , HOH B:5051 , HOH B:5111 , HOH B:5120 , HOH B:5178BINDING SITE FOR RESIDUE F6P B 4336
03AC3SOFTWAREGLU A:1097 , ASP A:1118 , ASP A:1121 , GLU A:1280 , PO4 A:3434BINDING SITE FOR RESIDUE MG A 3341
04AC4SOFTWAREGLU B:2097 , ASP B:2118 , ASP B:2121 , GLU B:2280 , F6P B:4336 , TL B:4352 , PO4 B:4434BINDING SITE FOR RESIDUE MG B 4341
05AC5SOFTWAREGLU A:1097 , ASP A:1118 , LEU A:1120 , ASP A:1121 , GLY A:1122 , SER A:1123 , F6P A:3336 , MG A:3341 , TL A:3352 , TL A:3353 , TL A:3354 , HOH A:5343BINDING SITE FOR RESIDUE PO4 A 3434
06AC6SOFTWAREGLU B:2097 , ASP B:2118 , LEU B:2120 , ASP B:2121 , GLY B:2122 , SER B:2123 , GLU B:2280 , F6P B:4336 , MG B:4341 , TL B:4351 , TL B:4352 , TL B:4353 , TL B:4354BINDING SITE FOR RESIDUE PO4 B 4434
07AC7SOFTWAREVAL A:1017 , GLU A:1020 , GLY A:1021 , THR A:1027 , GLY A:1028 , GLU A:1029 , MET A:1030 , THR A:1031 , LYS A:1112 , TYR A:1113 , VAL A:1160 , MET A:1177 , HOH A:5070 , HOH A:5199 , HOH A:5244 , HOH A:5410BINDING SITE FOR RESIDUE AMP A 3337
08AC8SOFTWARELYS A:1274 , GLU A:1280 , F6P A:3336 , TL A:3352BINDING SITE FOR RESIDUE TL A 3351
09AC9SOFTWAREGLU A:1097 , TL A:3351 , PO4 A:3434BINDING SITE FOR RESIDUE TL A 3352
10BC1SOFTWAREGLU A:1097 , GLU A:1098 , TL A:3354 , PO4 A:3434BINDING SITE FOR RESIDUE TL A 3353
11BC2SOFTWAREGLU A:1097 , GLU A:1098 , ASP A:1118 , LEU A:1120 , TL A:3353 , PO4 A:3434BINDING SITE FOR RESIDUE TL A 3354
12BC3SOFTWAREVAL B:2017 , GLU B:2020 , GLY B:2021 , THR B:2027 , GLY B:2028 , GLU B:2029 , MET B:2030 , THR B:2031 , LYS B:2112 , TYR B:2113 , ARG B:2140 , VAL B:2160 , MET B:2177 , HOH B:5127 , HOH B:5133 , HOH B:5259BINDING SITE FOR RESIDUE AMP B 4337
13BC4SOFTWAREGLU B:2280 , F6P B:4336 , TL B:4352 , PO4 B:4434BINDING SITE FOR RESIDUE TL B 4351
14BC5SOFTWAREGLU B:2097 , ARG B:2276 , GLU B:2280 , MG B:4341 , TL B:4351 , PO4 B:4434BINDING SITE FOR RESIDUE TL B 4352
15BC6SOFTWAREGLU B:2097 , GLU B:2098 , TL B:4354 , PO4 B:4434BINDING SITE FOR RESIDUE TL B 4353
16BC7SOFTWAREGLU B:2097 , GLU B:2098 , ASP B:2118 , LEU B:2120 , TL B:4353 , PO4 B:4434BINDING SITE FOR RESIDUE TL B 4354

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NV7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NV7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NV7)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FBPASEPS00124 Fructose-1-6-bisphosphatase active site.F16P1_PIG274-286
 
  2A:1273-1285
B:2273-2285
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FBPASEPS00124 Fructose-1-6-bisphosphatase active site.F16P1_PIG274-286
 
  2A:1273-1285
B:2273-2285
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FBPASEPS00124 Fructose-1-6-bisphosphatase active site.F16P1_PIG274-286
 
  4A:1273-1285
B:2273-2285

(-) Exons   (0, 0)

(no "Exon" information available for 1NV7)

(-) 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:327
 aligned with F16P1_PIG | P00636 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:327
                                    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       
           F16P1_PIG     10 NIVTLTRFVMEEGRKARGTGEMTQLLNSLCTAVKAISTAVRKAGIAHLYGIAGSTNVTGDQVKKLDVLSNDLVINVLKSSFATCVLVSEEDKNAIIVEPEKRGKYVVCFDPLDGSSNIDCLVSIGTIFGIYRKNSTDEPSEKDALQPGRNLVAAGYALYGSATMLVLAMVNGVNCFMLDPAIGEFILVDRDVKIKKKGSIYSINEGYAKEFDPAITEYIQRKKFPPDNSAPYGARYVGSMVADVHRTLVYGGIFMYPANKKSPKGKLRLLYECNPMAYVMEKAGGLATTGKEAVLDIVPTDIHQRAPIILGSPEDVTELLEIYQKHA  336
               SCOP domains d1nv7a_ A: Fructose-1,6-bisphosphatase                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1nv7A01 A:1009-1199 Fructose-1,6-Bisphosphatase, subunit A, domain 1                                                                                                                           1nv7A02 A:1200-1334  [code=3.40.190.80, no name defined]                                                                               - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhh..............hhhhhhhhhhhhhhhh...eeeeee......ee.hhh.eeeeeeeeeeeehhhhhhhh..eeeeeeeee.......hhhhhh.hhhhh.eeeeeee...eeeeeee..eeeeeee......eeeee..........eee.hhhhh...hhhhhhhhhhhhh........ee....hhhhhhhhhhhhh.eeee...............hhhhhhhhhhhh..eee....hhhhh..........eeeehhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FBPASE       -------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1nv7 A 1009 NIVTLTRFVMEEGRKARGTGEMTQLLNSLCTAVKAISTAVRKAGIAHLYGIAGSTNVTGDQVKKLDVLSNDLVINVLKSSFATCVLVSEEDKNAIIVEPEKRGKYVVCFDPLDGSSNIDCLVSIGTIFGIYRKNSTDEPSEKDALQPGRNLVAAGYALYGSATMLVLAMVNGVNCFMLDPAIGEFILVDRDVKIKKKGSIYSINEGYAKEFDPAITEYIQRKKFPPDNSAPYGARYVGSMVADVHRTLVYGGIFMYPANKKSPKGKLRLLYECNPMAYVMEKAGGLATTGKEAVLDIVPTDIHQRAPIILGSPEDVTELLEIYQKHA 1335
                                  1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148      1158      1168      1178      1188      1198      1208      1218      1228      1238      1248      1258      1268      1278      1288      1298      1308      1318      1328       

Chain B from PDB  Type:PROTEIN  Length:327
 aligned with F16P1_PIG | P00636 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:327
                                    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       
           F16P1_PIG     10 NIVTLTRFVMEEGRKARGTGEMTQLLNSLCTAVKAISTAVRKAGIAHLYGIAGSTNVTGDQVKKLDVLSNDLVINVLKSSFATCVLVSEEDKNAIIVEPEKRGKYVVCFDPLDGSSNIDCLVSIGTIFGIYRKNSTDEPSEKDALQPGRNLVAAGYALYGSATMLVLAMVNGVNCFMLDPAIGEFILVDRDVKIKKKGSIYSINEGYAKEFDPAITEYIQRKKFPPDNSAPYGARYVGSMVADVHRTLVYGGIFMYPANKKSPKGKLRLLYECNPMAYVMEKAGGLATTGKEAVLDIVPTDIHQRAPIILGSPEDVTELLEIYQKHA  336
               SCOP domains d1nv7b_ B: Fructose-1,6-bisphosphatase                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1nv7B01 B:2009-2199 Fructose-1,6-Bisphosphatase, subunit A, domain 1                                                                                                                           1nv7B02 B:2200-2334  [code=3.40.190.80, no name defined]                                                                               - CATH domains
           Pfam domains (1) --FBPase-1nv7B01 B:2011-2334                                                                                                                                                                                                                                                                                                          - Pfam domains (1)
           Pfam domains (2) --FBPase-1nv7B02 B:2011-2334                                                                                                                                                                                                                                                                                                          - Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhh..............hhhhhhhhhhhhhhhh...eeeeee......ee.hhh.eeeeeeeeeeeehhhhh.....eeeeeeeee.......hhhhhh.hhhhh.eeeeeee...eeeeeee..eeeeeeee....eeeeee..........eee.hhhhhhhhhhhhhhhhhhhhh........ee....hhhhhhhhhhhhh.eeee...............hhhhhhhhhhhh..eee....hhhhh..........eeeehhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FBPASE       -------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1nv7 B 2009 NIVTLTRFVMEEGRKARGTGEMTQLLNSLCTAVKAISTAVRKAGIAHLYGIAGSTNVTGDQVKKLDVLSNDLVINVLKSSFATCVLVSEEDKNAIIVEPEKRGKYVVCFDPLDGSSNIDCLVSIGTIFGIYRKNSTDEPSEKDALQPGRNLVAAGYALYGSATMLVLAMVNGVNCFMLDPAIGEFILVDRDVKIKKKGSIYSINEGYAKEFDPAITEYIQRKKFPPDNSAPYGARYVGSMVADVHRTLVYGGIFMYPANKKSPKGKLRLLYECNPMAYVMEKAGGLATTGKEAVLDIVPTDIHQRAPIILGSPEDVTELLEIYQKHA 2335
                                  2018      2028      2038      2048      2058      2068      2078      2088      2098      2108      2118      2128      2138      2148      2158      2168      2178      2188      2198      2208      2218      2228      2238      2248      2258      2268      2278      2288      2298      2308      2318      2328       

   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, 2)

Asymmetric Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Family: FBPase (32)
1aFBPase-1nv7B01B:2011-2334
1bFBPase-1nv7B02B:2011-2334

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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 1q9d 1rdx 1rdy 1rdz 1yxi 1yyz 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

1nuz COMPLEX WITH MAGNESIUM, FRUCTOSE-6-PHOSPHATE AND PHOSPHATE, AT 1.9A
1nv0 COMPLEX WITH MAGNESIUM, FRUCTOSE-6-PHOSPHATE, PHOSPHATE AND 1MM THALLIUM
1nv1 COMPLEX WITH MAGNESIUM, FRUCTOSE-6-PHOSPHATE, PHOSPHATE AND 5MM THALLIUM
1nv2 COMPLEX WITH MAGNESIUM, FRUCTOSE-6-PHOSPHATE, PHOSPHATE AND 20MM THALLIUM
1nv3 COMPLEX WITH MAGNESIUM, FRUCTOSE-6-PHOSPHATE, PHOSPHATE AND 100MM THALLIUM
1nv4 COMPLEX WITH MAGNESIUM, FRUCTOSE-6-PHOSPHATE, PHOSPHATE, EDTA AND 1MM THALLIUM
1nv5 COMPLEX WITH MAGNESIUM, FRUCTOSE-6-PHOSPHATE, PHOSPHATE, EDTA AND 5MM THALLIUM
1nv6 COMPLEX WITH MAGNESIUM, FRUCTOSE-6-PHOSPHATE, PHOSPHATE, EDTA AND 20MM THALLIUM