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(-) Description

Title :  THE BISPHOSPHATASE DOMAIN OF THE BIFUNCTIONAL RAT LIVER 6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE
 
Authors :  Y. -H. Lee, T. W. Olson, C. M. Ogata, D. G. Levitt, L. J. Banaszak, A. J. Lange
Date :  28 May 97  (Deposition) - 28 Jan 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Multifunctional Enzyme, Transferase, Kinase, Atp-Binding, Phosphorylation, Alternative Splicing, Multigene Family, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. H. Lee, T. W. Olson, C. M. Ogata, D. G. Levitt, L. J. Banaszak, A. J. Lange
Crystal Structure Of A Trapped Phosphoenzyme During A Catalytic Reaction.
Nat. Struct. Biol. V. 4 615 1997
PubMed-ID: 9253407  |  Reference-DOI: 10.1038/NSB0897-615
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOENZYME INTERMEDIATE OF FRU-2,6- BISPHOSPHATASE
    ChainsA, B
    EC Number3.1.3.46
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System GeneA CODING REGION WHICH COVERS FRUCTOSE-2,6-BISPHOSPHATASE DOMAIN (RESIDUES 251 - 440) OF THE RAT LIVER 6-PF-2-K/FRU-2,6-P2ASE (RESIDUES 1 - 470)
    Expression System PlasmidPET3A
    Expression System StrainDL41 DE3
    Expression System Taxid562
    GeneA CODING REGION WHICH COVERS
    MutationYES
    OrganLIVER
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymD-FRUCTOSE-2,6-BISPHOSPHATE 2-PHOSPHOHYDROLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1F6P2Ligand/IonFRUCTOSE-6-PHOSPHATE
2NEP2Mod. Amino AcidN1-PHOSPHONOHISTIDINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:20 , GLY A:21 , GLU A:78 , TYR A:89 , ARG A:103 , LYS A:107 , TYR A:118 , GLN A:144 , ARG A:148 , HOH A:501 , HOH A:549 , HOH A:612 , HOH A:614 , HOH A:702 , GLU B:90BINDING SITE FOR RESIDUE F6P A 401
2AC2SOFTWAREILE B:20 , GLU B:78 , TYR B:89 , ARG B:103 , LYS B:107 , TYR B:118 , GLN B:144 , ARG B:148 , HOH B:502 , HOH B:532 , HOH B:534 , HOH B:571 , HOH B:575 , HOH B:581 , HOH B:721BINDING SITE FOR RESIDUE F6P B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PG_MUTASEPS00175 Phosphoglycerate mutase family phosphohistidine signature.F261_RAT256-265
 
  2A:6-15
B:6-15

(-) Exons   (6, 12)

Asymmetric/Biological Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENSRNOT000000336562ENSRNOE00000000951X:39838444-39838739296F261_RAT1-33330--
1.4ENSRNOT000000336564ENSRNOE00000272281X:39853712-39853837126F261_RAT33-75430--
1.5ENSRNOT000000336565ENSRNOE00000272273X:39861462-3986155594F261_RAT75-106320--
1.6ENSRNOT000000336566ENSRNOE00000272265X:39862515-3986258167F261_RAT106-128230--
1.7ENSRNOT000000336567ENSRNOE00000000955X:39863632-3986370675F261_RAT129-153250--
1.8ENSRNOT000000336568ENSRNOE00000000956X:39864124-3986418057F261_RAT154-172190--
1.9ENSRNOT000000336569ENSRNOE00000272256X:39867100-39867221122F261_RAT173-213410--
1.10ENSRNOT0000003365610ENSRNOE00000272245X:39870859-39871066208F261_RAT213-282702A:1-32
B:1-32
32
32
1.11ENSRNOT0000003365611ENSRNOE00000000959X:39874025-39874171147F261_RAT283-331492A:33-81
B:33-81
49
49
1.12ENSRNOT0000003365612ENSRNOE00000000960X:39876381-39876485105F261_RAT332-366352A:82-116
B:82-116
35
35
1.13ENSRNOT0000003365613ENSRNOE00000272236X:39881174-39881303130F261_RAT367-410442A:117-160
B:117-160
44
44
1.14ENSRNOT0000003365614ENSRNOE00000272297X:39884092-3988415463F261_RAT410-431222A:160-181
B:160-181
22
22
1.15ENSRNOT0000003365615ENSRNOE00000272289X:39885373-3988543765F261_RAT431-452222A:181-191
B:181-191
11
11
1.16ENSRNOT0000003365616ENSRNOE00000272818X:39885770-39886105336F261_RAT453-471190--

(-) 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:191
 aligned with F261_RAT | P07953 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:191
                                   260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440 
             F261_RAT   251 PRSIYLCRHGESELNLRGRIGGDSGLSARGKQYAYALANFIRSQGISSLKVWTSHMKRTIQTAEALGVPYEQWKALNEIDAGVCEEMTYEEIQEHYPEEFALRDQDKYRYRYPKGESYEDLVQRLEPVIMELERQENVLVICHQAVMRCLLAYFLDKSSDELPYLKCPLHTVLKLTPVAYGCRVESIYLNV 441
               SCOP domains d1tipa_ A: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain                                                                                                             SCOP domains
               CATH domains 1tipA00 A:1-191 Phosphoglycerate mutase-like                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....hhhh...........hhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhh....eeehhh.....hhh....hhhhhhh.hhhhhhhhh............hhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhh....hhhhhh......eeeeeeee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PG_MUTASE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.10  PDB: A:1-32          Exon 1.11  PDB: A:33-81 UniProt: 283-331         Exon 1.12  PDB: A:82-116           Exon 1.13  PDB: A:117-160 UniProt: 367-410  --------------------Exon 1.15   Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.14             ---------- Transcript 1 (2)
                 1tip A   1 MRSIYLCRhGESELNLRGRIGGDSGLSARGKQYAYALANFIRSQGISSLKVWTSHMKRTIQTAEALGVPYEQWKALNEIDAGVCEEMTYEEIQEHYPEEFALRDQDKYRYRYPKGESYEDLVQRLEPVIMELERQENVLVICHQAVMRCLLAYFLDKSSDELPYLKCPLHTVLKLTPVAYGCRVESIYLNV 191
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190 
                                    9-NEP                                                                                                                                                                                  

Chain B from PDB  Type:PROTEIN  Length:191
 aligned with F261_RAT | P07953 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:191
                                   260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440 
             F261_RAT   251 PRSIYLCRHGESELNLRGRIGGDSGLSARGKQYAYALANFIRSQGISSLKVWTSHMKRTIQTAEALGVPYEQWKALNEIDAGVCEEMTYEEIQEHYPEEFALRDQDKYRYRYPKGESYEDLVQRLEPVIMELERQENVLVICHQAVMRCLLAYFLDKSSDELPYLKCPLHTVLKLTPVAYGCRVESIYLNV 441
               SCOP domains d1tipb_ B: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain                                                                                                             SCOP domains
               CATH domains 1tipB00 B:1-191 Phosphoglycerate mutase-like                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....hhhh...........hhhhhhhhhhhhhhhhh.....eee....hhhhhhhhh........hhh.....hhh....hhhhhhh.hhhhhhhhhh...........hhhhhhh.hhhhhhhhh...eeee..hhhhhhhhhhh....hhhhhh......eeeeeee....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PG_MUTASE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.10  PDB: B:1-32          Exon 1.11  PDB: B:33-81 UniProt: 283-331         Exon 1.12  PDB: B:82-116           Exon 1.13  PDB: B:117-160 UniProt: 367-410  --------------------Exon 1.15   Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.14             ---------- Transcript 1 (2)
                 1tip B   1 MRSIYLCRhGESELNLRGRIGGDSGLSARGKQYAYALANFIRSQGISSLKVWTSHMKRTIQTAEALGVPYEQWKALNEIDAGVCEEMTYEEIQEHYPEEFALRDQDKYRYRYPKGESYEDLVQRLEPVIMELERQENVLVICHQAVMRCLLAYFLDKSSDELPYLKCPLHTVLKLTPVAYGCRVESIYLNV 191
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190 
                                    9-NEP                                                                                                                                                                                  

   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/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 30)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (F261_RAT | P07953)
molecular function
    GO:0003873    6-phosphofructo-2-kinase activity    Catalysis of the reaction: beta-D-fructose 6-phosphate + ATP = beta-D-fructose 2,6-bisphosphate + ADP + 2 H(+).
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0004331    fructose-2,6-bisphosphate 2-phosphatase activity    Catalysis of the reaction: D-fructose 2,6-bisphosphate + H2O = D-fructose-6-phosphate + phosphate.
    GO:0070095    fructose-6-phosphate binding    Interacting selectively and non-covalently with fructose 6-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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0019900    kinase binding    Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
    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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0031100    animal organ regeneration    The regrowth of a lost or destroyed animal organ.
    GO:0061621    canonical glycolysis    The glycolytic process that begins with the conversion of glucose to glucose-6-phosphate by glucokinase activity. Glycolytic processes are the chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP.
    GO:0046835    carbohydrate phosphorylation    The process of introducing a phosphate group into a carbohydrate, any organic compound based on the general formula Cx(H2O)y.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0006112    energy reserve metabolic process    The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen.
    GO:0006003    fructose 2,6-bisphosphate metabolic process    The chemical reactions and pathways involving fructose 2,6-bisphosphate. The D enantiomer is an important regulator of the glycolytic and gluconeogenic pathways. It inhibits fructose 1,6-bisphosphatase and activates phosphofructokinase.
    GO:0006000    fructose metabolic process    The chemical reactions and pathways involving fructose, the ketohexose arabino-2-hexulose. Fructose exists in a open chain form or as a ring compound. D-fructose is the sweetest of the sugars and is found free in a large number of fruits and honey.
    GO:0006094    gluconeogenesis    The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    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:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0033133    positive regulation of glucokinase activity    Any process that activates or increases the frequency, rate or extent of glucokinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a glucose molecule.
    GO:0051591    response to cAMP    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
    GO:0033762    response to glucagon    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucagon stimulus.
    GO:0051384    response to glucocorticoid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
    GO:0032868    response to insulin    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0042594    response to starvation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a starvation stimulus, deprivation of nourishment.
cellular component
    GO:0043540    6-phosphofructo-2-kinase/fructose-2,6-biphosphatase complex    A homodimeric, bifunctional enzyme complex which catalyzes the synthesis and degradation of fructose 2,6-bisphosphate, and is required for both glycolysis and gluconeogenesis.
    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
        F261_RAT | P079531c7z 1c80 1c81 1fbt

(-) Related Entries Specified in the PDB File

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