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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX OF PHOSPHOFRUCTOKINASE FROM ESCHERICHIA COLI WITH ITS REACTION PRODUCTS
 
Authors :  Y. Shirakihara, P. R. Evans
Date :  25 Jan 88  (Deposition) - 09 Jan 89  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Transferase(Phosphotransferase) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Shirakihara, P. R. Evans
Crystal Structure Of The Complex Of Phosphofructokinase Fro Escherichia Coli With Its Reaction Products.
J. Mol. Biol. V. 204 973 1988
PubMed-ID: 2975709  |  Reference-DOI: 10.1016/0022-2836(88)90056-3
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOFRUCTOKINASE
    Cell Line293
    ChainsA, B
    EC Number2.7.1.11
    EngineeredYES
    Expression System Strain293
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE
2FBP2Ligand/IonBETA-FRUCTOSE-1,6-DIPHOSPHATE
3MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1ADP8Ligand/IonADENOSINE-5'-DIPHOSPHATE
2FBP4Ligand/IonBETA-FRUCTOSE-1,6-DIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:11 , ARG A:72 , THR A:125 , ASP A:127 , MET A:169 , GLY A:170 , ARG A:171 , GLU A:222 , HIS A:249 , ARG A:252 , ADP A:324 , MG A:325 , HOH A:330 , HOH A:351 , HOH A:402 , HOH A:417 , HOH A:430 , HOH A:447 , ARG B:162 , ARG B:243BINDING SITE FOR RESIDUE FBP A 323
02AC2SOFTWAREARG A:162 , ARG A:243 , GLY B:11 , THR B:125 , ASP B:127 , MET B:169 , GLY B:170 , ARG B:171 , GLU B:222 , HIS B:249 , ARG B:252 , ADP B:324 , HOH B:331 , HOH B:352 , HOH B:387 , HOH B:403 , HOH B:447 , HOH B:448BINDING SITE FOR RESIDUE FBP B 323
03AC3SOFTWAREASP A:103 , FBP A:323 , ADP A:324 , HOH A:386 , HOH A:402 , HOH A:417BINDING SITE FOR RESIDUE MG A 325
04AC4SOFTWAREGLY A:185 , GLU A:187 , ADP A:326 , HOH A:368 , HOH A:369BINDING SITE FOR RESIDUE MG A 327
05AC5SOFTWAREASP B:103 , ADP B:324 , HOH B:419BINDING SITE FOR RESIDUE MG B 325
06AC6SOFTWAREGLY B:185 , GLU B:187 , ADP B:326 , HOH B:369 , HOH B:370BINDING SITE FOR RESIDUE MG B 327
07AC7SOFTWAREGLY A:10 , GLY A:11 , TYR A:41 , ARG A:72 , PHE A:73 , PHE A:76 , ARG A:77 , GLY A:102 , ASP A:103 , GLY A:104 , SER A:105 , MET A:107 , GLY A:108 , FBP A:323 , MG A:325 , HOH A:351 , HOH A:365 , HOH A:386 , HOH A:465BINDING SITE FOR RESIDUE ADP A 324
08AC8SOFTWAREARG A:154 , SER A:158 , GLY A:185 , GLU A:187 , GLY A:212 , LYS A:213 , LYS A:214 , HIS A:215 , MG A:327 , HOH A:368 , HOH A:369 , HOH A:467 , ARG B:21 , ARG B:25 , ARG B:54 , TYR B:55 , SER B:58 , ASP B:59 , HOH B:420BINDING SITE FOR RESIDUE ADP A 326
09AC9SOFTWARESER B:9 , TYR B:41 , ARG B:72 , PHE B:73 , PRO B:74 , PHE B:76 , ARG B:77 , GLY B:102 , ASP B:103 , GLY B:104 , SER B:105 , MET B:107 , GLY B:108 , FBP B:323 , MG B:325 , HOH B:366BINDING SITE FOR RESIDUE ADP B 324
10BC1SOFTWAREARG A:21 , ARG A:25 , ARG A:54 , TYR A:55 , SER A:58 , ASP A:59 , HOH A:419 , ARG B:154 , SER B:158 , GLY B:185 , GLU B:187 , GLY B:212 , LYS B:213 , LYS B:214 , HIS B:215 , MG B:327 , HOH B:328 , HOH B:369 , HOH B:370BINDING SITE FOR RESIDUE ADP B 326

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PHOSPHOFRUCTOKINASEPS00433 Phosphofructokinase signature.PFKA_ECOLI244-262
 
  2A:243-261
B:243-261
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PHOSPHOFRUCTOKINASEPS00433 Phosphofructokinase signature.PFKA_ECOLI244-262
 
  4A:243-261
B:243-261

(-) Exons   (0, 0)

(no "Exon" information available for 1PFK)

(-) 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:320
 aligned with PFKA_ECOLI | P0A796 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:320
                                    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
           PFKA_ECOLI     1 MIKKIGVLTSGGDAPGMNAAIRGVVRSALTEGLEVMGIYDGYLGLYEDRMVQLDRYSVSDMINRGGTFLGSARFPEFRDENIRAVAIENLKKRGIDALVVIGGDGSYMGAMRLTEMGFPCIGLPGTIDNDIKGTDYTIGFFTALSTVVEAIDRLRDTSSSHQRISVVEVMGRYCGDLTLAAAIAGGCEFVVVPEVEFSREDLVNEIKAGIAKGKKHAIVAITEHMCDVDELAHFIEKETGRETRATVLGHIQRGGSPVPYDRILASRMGAYAIDLLLAGYGGRCVGIQNEQLVHHDIIDAIENMKRPFKGDWLDCAKKLY 320
               SCOP domains d1pfka_ A: ATP-dependent phosphofructokinase                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1pfkA01 A:0-141,A:256-302  [code=3.40.50.450, no name defined]                                                                                1pfkA02 A:142-251,A:303-318  [code=3.40.50.460, no name defined]                                              ----1pfkA01 A:0-141,A:256-302                      1pfkA02         - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ..eeeeeeee.....hhhhhhhhhhhhhhhh..eeeeee.hhhhhhhheeeee....................hhhhhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhh.eeeee...............hhhhhhhhhhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhh..eee......hhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh.eeeeeeehhhhh....hhhhhhhhhhhhhhhhhhhhhh..eeeeeee..-----hhhhhhhh.....hhhhhhhhhhhh Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------eeeeee------------------------ Sec.struct. author (2)
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PHOSPHOFRUCTOKINASE---------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pfk A   0 MIKKIGVLTSGGDAPGMNAAIRGVVRSALTEGLEVMGIYDGYLGLYEDRMVQLDRYSVSDMINRGGTFLGSARFPEFRDENIRAVAIENLKKRGIDALVVIGGDGSYMGAMRLTEMGFPCIGLPGTIDNDIKGTDYTIGFFTALSTVVEAIDRLRDTSSSHQRISVVEVMGRYCGDLTLAAAIAGGCEFVVVPEVEFSREDLVNEIKAGIAKGKKHAIVAITEHMCDVDELAHFIEKETGRETRATVLGHIQRGGSPVPYDRILASRMGAYAIDLLLAGYGGRCVGIQNEQLVHHDIIDAIENMKRPFKGDWLDCAKKLY 319
                                     9        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

Chain B from PDB  Type:PROTEIN  Length:320
 aligned with PFKA_ECOLI | P0A796 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:320
                                    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
           PFKA_ECOLI     1 MIKKIGVLTSGGDAPGMNAAIRGVVRSALTEGLEVMGIYDGYLGLYEDRMVQLDRYSVSDMINRGGTFLGSARFPEFRDENIRAVAIENLKKRGIDALVVIGGDGSYMGAMRLTEMGFPCIGLPGTIDNDIKGTDYTIGFFTALSTVVEAIDRLRDTSSSHQRISVVEVMGRYCGDLTLAAAIAGGCEFVVVPEVEFSREDLVNEIKAGIAKGKKHAIVAITEHMCDVDELAHFIEKETGRETRATVLGHIQRGGSPVPYDRILASRMGAYAIDLLLAGYGGRCVGIQNEQLVHHDIIDAIENMKRPFKGDWLDCAKKLY 320
               SCOP domains d1pfkb_ B: ATP-dependent phosphofructokinase                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1pfkB01 B:0-141,B:256-302  [code=3.40.50.450, no name defined]                                                                                1pfkB02 B:142-251,B:303-318  [code=3.40.50.460, no name defined]                                              ----1pfkB01 B:0-141,B:256-302                      1pfkB02         - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ..eeeeeeee.....hhhhhhhhhhhhhhhh..eeeeee.hhhhhhhheeeee....................hhhhhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhh.eeeee...............hhhhhhhhhhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhh..eee......hhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh.eeeeeeehhhhh....hhhhhhhhhhhhhhhhhhhhhh..eeeeeee..-----hhhhhhhh.....hhhhhhhhhhhh Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------eeeeee------------------------ Sec.struct. author (2)
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PHOSPHOFRUCTOKINASE---------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pfk B   0 MIKKIGVLTSGGDAPGMNAAIRGVVRSALTEGLEVMGIYDGYLGLYEDRMVQLDRYSVSDMINRGGTFLGSARFPEFRDENIRAVAIENLKKRGIDALVVIGGDGSYMGAMRLTEMGFPCIGLPGTIDNDIKGTDYTIGFFTALSTVVEAIDRLRDTSSSHQRISVVEVMGRYCGDLTLAAAIAGGCEFVVVPEVEFSREDLVNEIKAGIAKGKKHAIVAITEHMCDVDELAHFIEKETGRETRATVLGHIQRGGSPVPYDRILASRMGAYAIDLLLAGYGGRCVGIQNEQLVHHDIIDAIENMKRPFKGDWLDCAKKLY 319
                                     9        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

   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  (0, 0)

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

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PFKA_ECOLI | P0A796)
molecular function
    GO:0003872    6-phosphofructokinase activity    Catalysis of the reaction: ATP + D-fructose-6-phosphate = ADP + D-fructose 1,6-bisphosphate.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0019003    GDP binding    Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate.
    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: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: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:0008443    phosphofructokinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a fructose substrate molecule.
    GO:0032553    ribonucleotide binding    Interacting selectively and non-covalently with a ribonucleotide, any compound consisting of a ribonucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose moiety.
    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: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:0044275    cellular carbohydrate catabolic process    The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells.
    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:0006007    glucose catabolic process    The chemical reactions and pathways resulting in the breakdown of glucose, the aldohexose gluco-hexose.
    GO:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
    GO:0061615    glycolytic process through fructose-6-phosphate    The chemical reactions and pathways resulting in the breakdown of a monosaccharide into pyruvate, occurring through a fructose-6-phosphate intermediate, with the concomitant production of ATP and NADH.
    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:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
cellular component
    GO:0005945    6-phosphofructokinase complex    A protein complex that possesses 6-phosphofructokinase activity; homodimeric, homooctameric, and allosteric homotetrameric forms are known.
    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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