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(-) Description

Title :  PFKFB3 TRAPPED IN A PHOSPHO-ENZYME INTERMEDIATE STATE
 
Authors :  M. C. Cavalier, S. G. Kim, D. Neau, Y. H. Lee
Date :  14 Feb 11  (Deposition) - 08 Feb 12  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Kinase/Bisphosphatase, Transferase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. C. Cavalier, S. G. Kim, D. Neau, Y. H. Lee
Molecular Basis Of The Fructose-2, 6-Bisphosphatase Reaction Of Pfkfb3: Transition State And The C-Terminal Function.
Proteins V. 80 1143 2012
PubMed-ID: 22275052  |  Reference-DOI: 10.1002/PROT.24015

(-) Compounds

Molecule 1 - 6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE 3
    ChainsA
    EC Number2.7.1.105, 3.1.3.46
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GenePFKFB3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Synonym6PF-2-K/FRU-2,6-P2ASE 3, PFK/FBPASE 3, 6PF-2-K/FRU-2,6-P2ASE BRAIN/PLACENTA-TYPE ISOZYME, RENAL CARCINOMA ANTIGEN NY-REN-56, IPFK- 2, 6-PHOSPHOFRUCTO-2-KINASE, FRUCTOSE-2,6-BISPHOSPHATASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2F6P1Ligand/IonFRUCTOSE-6-PHOSPHATE
3FDP1Ligand/IonFRUCTOSE-2,6-DIPHOSPHATE
4PHS1Ligand/IonPHOSPHONIC ACID
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2F6P2Ligand/IonFRUCTOSE-6-PHOSPHATE
3FDP2Ligand/IonFRUCTOSE-2,6-DIPHOSPHATE
4PHS2Ligand/IonPHOSPHONIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:69 , GLY A:71 , ARG A:74 , ARG A:98 , ALA A:125 , THR A:126 , ASN A:127 , ARG A:132 , LYS A:168 , ARG A:189 , TYR A:193 , HOH A:530 , HOH A:553 , HOH A:564 , HOH A:588 , HOH A:604 , HOH A:605BINDING SITE FOR RESIDUE FDP A 524
2AC2SOFTWAREARG A:252 , HIS A:253 , ASN A:259 , HIS A:387 , GLN A:388 , HOH A:548 , HOH A:552 , F6P A:720BINDING SITE FOR RESIDUE PHS A 710
3AC3SOFTWAREPRO A:43 , ALA A:44 , ARG A:45 , GLY A:46 , LYS A:47 , THR A:48 , TYR A:49 , SER A:152 , ASN A:163 , VAL A:167 , LYS A:168 , VAL A:217 , TYR A:424 , HOH A:633BINDING SITE FOR RESIDUE ADP A 700
4AC4SOFTWAREILE A:264 , GLY A:265 , GLU A:322 , TYR A:333 , ARG A:347 , LYS A:351 , TYR A:362 , GLN A:388 , ARG A:392 , HOH A:533 , HOH A:536 , HOH A:538 , HOH A:543 , HOH A:548 , HOH A:570 , HOH A:652 , PHS A:710BINDING SITE FOR RESIDUE F6P A 720

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QPV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3QPV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QPV)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PG_MUTASEPS00175 Phosphoglycerate mutase family phosphohistidine signature.F263_HUMAN251-260  1A:250-259
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PG_MUTASEPS00175 Phosphoglycerate mutase family phosphohistidine signature.F263_HUMAN251-260  2A:250-259

(-) Exons   (14, 14)

Asymmetric Unit (14, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3dENST000003797753dENSE00001911115chr10:6244894-6245299406F263_HUMAN1-26261A:3-2018
1.4ENST000003797754ENSE00001636131chr10:6255586-6255711126F263_HUMAN26-68431A:32-6736
1.5ENST000003797755ENSE00001691710chr10:6257184-625728097F263_HUMAN68-100331A:67-9933
1.6ENST000003797756ENSE00001625550chr10:6258088-625815467F263_HUMAN100-122231A:99-12123
1.7ENST000003797757ENSE00001748558chr10:6258669-625874375F263_HUMAN123-147251A:122-14625
1.8ENST000003797758ENSE00001650689chr10:6259098-625915457F263_HUMAN148-166191A:147-16519
1.9ENST000003797759ENSE00001672633chr10:6261532-6261656125F263_HUMAN167-208421A:166-20742
1.10ENST0000037977510ENSE00001727947chr10:6262621-6262828208F263_HUMAN208-277701A:207-27670
1.11aENST0000037977511aENSE00001665756chr10:6263344-6263490147F263_HUMAN278-326491A:277-32549
1.12ENST0000037977512ENSE00001758318chr10:6263604-6263708105F263_HUMAN327-361351A:326-36035
1.13bENST0000037977513bENSE00001626155chr10:6264818-6264947130F263_HUMAN362-405441A:361-40444
1.14ENST0000037977514ENSE00001771643chr10:6265921-626598363F263_HUMAN405-426221A:404-42522
1.15aENST0000037977515aENSE00001800461chr10:6266112-626617665F263_HUMAN426-447221A:425-44622
1.18aENST0000037977518aENSE00001683359chr10:6268155-6268328174F263_HUMAN448-505581A:453-4597
1.22gENST0000037977522gENSE00001643662chr10:6274858-62774952638F263_HUMAN506-520150--

(-) 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:440
 aligned with F263_HUMAN | Q16875 from UniProtKB/Swiss-Prot  Length:520

    Alignment length:457
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       
           F263_HUMAN     4 ELTQSRVQKIWVPVDHRPSLPRSCGPKLTNSPTVIVMVGLPARGKTYISKKLTRYLNWIGVPTKVFNVGEYRREAVKQYSSYNFFRPDNEEAMKVRKQCALAALRDVKSYLAKEGGQIAVFDATNTTRERRHMILHFAKENDFKAFFIESVCDDPTVVASNIMEVKISSPDYKDCNSAEAMDDFMKRISCYEASYQPLDPDKCDRDLSLIKVIDVGRRFLVNRVQDHIQSRIVYYLMNIHVQPRTIYLCRHGENEHNLQGRIGGDSGLSSRGKKFASALSKFVEEQNLKDLRVWTSQLKSTIQTAEALRLPYEQWKALNEIDAGVCEELTYEEIRDTYPEEYALREQDKYYYRYPTGESYQDLVQRLEPVIMELERQENVLVICHQAVLRCLLAYFLDKSAEEMPYLKCPLHTVLKLTPVAYGCRVESIYLNVESVCTHRERSEDAKKGPNPLMRRN 460
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee......ee......-----------...eeeeee.....hhhhhhhhhhhhhhhh...eeeeehhhhhhhhh....hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhh...............eeeee....eeeee...hhhhhhhhhhhh........eeeee...hhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhh.....ee.hhhh...hhhhh..hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhh.....hhhhh.....eeeeeeee..eeeeeeee..............------hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PG_MUTASE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3d  PDB: A:3-20 -----------------------------------------Exon 1.5  PDB: A:67-99           ----------------------Exon 1.7  PDB: A:122-146 Exon 1.8           -----------------------------------------Exon 1.10  PDB: A:207-276 UniProt: 208-277                            Exon 1.11a  PDB: A:277-325 UniProt: 278-326      Exon 1.12  PDB: A:326-360          Exon 1.13b  PDB: A:361-404 UniProt: 362-405 --------------------Exon 1.15a            Exon 1.18a    Transcript 1 (1)
           Transcript 1 (2) ----------------------Exon 1.4  PDB: A:32-67 UniProt: 26-68      -------------------------------Exon 1.6  PDB: A:99-121--------------------------------------------Exon 1.9  PDB: A:166-207 UniProt: 167-208 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.14             ---------------------------------- Transcript 1 (2)
                 3qpv A   3 ELTQSRVQKIWVPVDHRP-----------NSPTVIVMVGLPARGKTYISKKLTRYLNWIGVPTKVFNVGEYRREAVKQYSSYNFFRPDNEEAMKVRKQCALAALRDVKSYLAKEGGQIAVFDATNTTRERRHMILHFAKENDFKAFFIESVCDDPTVVASNIMEVKISSPDYKDCNSAEAMDDFMKRISCYEASYQPLDPDKCDRDLSLIKVIDVGRRFLVNRVQDHIQSRIVYYLMNIHVQPRTIYLCRHGENEHNLQGRIGGDSGLSSRGKKFASALSKFVEEQNLKDLRVWTSQLKSTIQTAEALRLPYEQWKALNEIDAGVCEELTYEEIRDTYPEEYALREQDKYYYRYPTGESYQDLVQRLEPVIMELERQENVLVICHQAVLRCLLAYFLDKSAEEMPYLKCPLHTVLKLTPVAYGCRVESIYLNVESVCTHRERSE------NPLMRRN 459
                                    12       | -        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442   |     -|      
                                            20          32                                                                                                                                                                                                                                                                                                                                                                                                                           446    453      

   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  (0, 0)

(no "SCOP Domain" information available for 3QPV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QPV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QPV)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A   (F263_HUMAN | Q16875)
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: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:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    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: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: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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        F263_HUMAN | Q168752axn 2dwo 2dwp 2i1v 3qpu 3qpw 4d4j 4d4k 4d4l 4d4m 4ma4 5ajv 5ajw 5ajx 5ajy 5ajz 5ak0

(-) Related Entries Specified in the PDB File

3qpu 3qpw