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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PHOSPHOFRUCTOKINASE-2 FROM ESCHERICHIA COLI IN COMPLEX WITH POTASSIUM
 
Authors :  H. M. Pereira, A. Caniuguir, M. Baez, R. Cabrera, R. C. Garratt, J. Babul
Date :  14 Nov 11  (Deposition) - 14 Nov 12  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Glycolysis, Transferase, Pfk, Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Baez, R. Cabrera, H. M. Pereira, A. Blanco, P. Villalobos, C. A. Ramirez-Sarmiento, A. Caniuguir, V. Guixe, R. C. Garratt, J. Babul
A Ribokinase Family Conserved Monovalent Cation Binding Sit Enhances The Mgatp-Induced Inhibition In E. Coli Phosphofructokinase-2
Biophys. J. V. 105 185 2013
PubMed-ID: 23823238  |  Reference-DOI: 10.1016/J.BPJ.2013.05.028

(-) Compounds

Molecule 1 - 6-PHOSPHOFRUCTOKINASE ISOZYME 2
    ChainsA, B
    EC Number2.7.1.11
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21-D
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneB1723, JW5280, PFK2, PFKB
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK12
    SynonymPHOSPHOFRUCTOKINASE-2

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1ATP4Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2K2Ligand/IonPOTASSIUM ION
3MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1ATP8Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2K-1Ligand/IonPOTASSIUM ION
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1ATP4Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2K-1Ligand/IonPOTASSIUM ION
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREATP A:313 , HOH A:532 , HOH A:533 , HOH A:535 , HOH B:534BINDING SITE FOR RESIDUE MG A 310
02AC2SOFTWAREATP A:313 , HOH A:686 , ATP B:312 , HOH B:531BINDING SITE FOR RESIDUE MG A 311
03AC3SOFTWARELYS A:185 , ASN A:187 , SER A:224 , LEU A:225 , GLY A:226 , PRO A:227 , GLY A:229 , THR A:251 , ALA A:254 , GLY A:255 , MET A:258 , VAL A:280 , GLY A:283 , SER A:284 , THR A:287 , MG A:310 , MG A:311 , HOH A:320 , HOH A:323 , HOH A:326 , HOH A:360 , HOH A:516 , HOH A:518 , HOH A:532 , HOH A:533 , HOH A:535 , HOH A:649 , HOH A:686 , LYS B:27 , ATP B:312 , HOH B:531BINDING SITE FOR RESIDUE ATP A 313
04AC4SOFTWARESER A:250 , VAL A:252 , ALA A:286 , ASN A:289 , GLY A:291 , ARG A:293BINDING SITE FOR RESIDUE K A 314
05AC5SOFTWAREATP A:315 , HOH A:536 , ATP B:313 , HOH B:669BINDING SITE FOR RESIDUE MG A 312
06AC6SOFTWARETYR A:23 , PRO A:24 , GLY A:26 , LYS A:27 , GLU A:102 , MG A:312 , HOH A:339 , HOH A:344 , HOH A:348 , HOH A:382 , HOH A:437 , HOH A:514 , HOH A:529 , HOH A:536 , HOH A:682 , ASN B:187 , LYS B:189 , GLY B:226 , PRO B:227 , THR B:251 , ATP B:313 , HOH B:452BINDING SITE FOR RESIDUE ATP A 315
07AC7SOFTWAREASN A:187 , LYS A:189 , GLY A:226 , THR A:251 , MG A:311 , ATP A:313 , HOH A:358 , HOH A:547 , TYR B:23 , GLY B:26 , LYS B:27 , GLU B:102 , HOH B:386 , HOH B:418 , HOH B:423 , HOH B:434 , HOH B:463 , HOH B:480 , HOH B:508 , HOH B:531 , HOH B:534 , HOH B:582 , HOH B:591BINDING SITE FOR RESIDUE ATP B 312
08AC8SOFTWAREHOH A:339 , HOH B:310 , ATP B:313 , HOH B:318 , HOH B:342BINDING SITE FOR RESIDUE MG B 311
09AC9SOFTWARELYS A:27 , MG A:312 , ATP A:315 , HOH A:339 , HOH A:536 , LYS B:185 , ASN B:187 , SER B:224 , LEU B:225 , GLY B:226 , PRO B:227 , GLY B:229 , ALA B:254 , GLY B:255 , MET B:258 , VAL B:280 , GLY B:283 , SER B:284 , THR B:287 , HOH B:310 , MG B:311 , HOH B:318 , HOH B:325 , HOH B:342 , HOH B:344 , HOH B:352 , HOH B:412 , HOH B:441 , HOH B:548 , HOH B:557 , HOH B:669BINDING SITE FOR RESIDUE ATP B 313
10BC1SOFTWARESER B:250 , VAL B:252 , ALA B:286 , ASN B:289 , GLY B:291 , ARG B:293BINDING SITE FOR RESIDUE K B 314

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PFKB_KINASES_1PS00583 pfkB family of carbohydrate kinases signature 1.PFKB_ECOLI38-62
 
  2A:38-62
B:38-62
2PFKB_KINASES_2PS00584 pfkB family of carbohydrate kinases signature 2.PFKB_ECOLI250-263
 
  2A:250-263
B:250-263
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PFKB_KINASES_1PS00583 pfkB family of carbohydrate kinases signature 1.PFKB_ECOLI38-62
 
  4A:38-62
B:38-62
2PFKB_KINASES_2PS00584 pfkB family of carbohydrate kinases signature 2.PFKB_ECOLI250-263
 
  4A:250-263
B:250-263
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PFKB_KINASES_1PS00583 pfkB family of carbohydrate kinases signature 1.PFKB_ECOLI38-62
 
  2A:38-62
B:38-62
2PFKB_KINASES_2PS00584 pfkB family of carbohydrate kinases signature 2.PFKB_ECOLI250-263
 
  2A:250-263
B:250-263

(-) Exons   (0, 0)

(no "Exon" information available for 3UMO)

(-) 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:309
 aligned with PFKB_ECOLI | P06999 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:309
                                    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         
           PFKB_ECOLI     1 MVRIYTLTLAPSLDSATITPQIYPEGKLRCTAPVFEPGGGGINVARAIAHLGGSATAIFPAGGATGEHLVSLLADENVPVATVEAKDWTRQNLHVHVEASGEQYRFVMPGAALNEDEFRQLEEQVLEIESGAILVISGSLPPGVKLEKLTQLISAAQKQGIRCIVDSSGEALSAALAIGNIELVKPNQKELSALVNRELTQPDDVRKAAQEIVNSGKAKRVVVSLGPQGALGVDSENCIQVVPPPVKSQSTVGAGDSMVGAMTLKLAENASLEEMVRFGVAAGSAATLNQGTRLCSHDDTQKIYAYLSR 309
               SCOP domains d3umoa_ A: automated matches                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....eeeeeeee.......eee....eeeeehhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhhh...eeeee........eeeee.....eeeee......hhhhhhhhhhhhh......eeeee.......hhhhhhhhhhhhhhh..eeeee.hhhhhhhhh......ee..hhhhhhhhhh......hhhhhhhhhhhhh.....eeee.hhh.eeee....eeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------PFKB_KINASES_1           -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2---------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3umo A   1 MVRIYTLTLAPSLDSATITPQIYPEGKLRCTAPVFEPGGGGINVARAIAHLGGSATAIFPAGGATGEHLVSLLADENVPVATVEAKDWTRQNLHVHVEASGEQYRFVMPGAALNEDEFRQLEEQVLEIESGAILVISGSLPPGVKLEKLTQLISAAQKQGIRCIVDSSGEALSAALAIGNIELVKPNQKELSALVNRELTQPDDVRKAAQEIVNSGKAKRVVVSLGPQGALGVDSENCIQVVPPPVKSQSTVGAGDSMVGAMTLKLAENASLEEMVRFGVAAGSAATLNQGTRLCSHDDTQKIYAYLSR 309
                                    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         

Chain B from PDB  Type:PROTEIN  Length:309
 aligned with PFKB_ECOLI | P06999 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:309
                                    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         
           PFKB_ECOLI     1 MVRIYTLTLAPSLDSATITPQIYPEGKLRCTAPVFEPGGGGINVARAIAHLGGSATAIFPAGGATGEHLVSLLADENVPVATVEAKDWTRQNLHVHVEASGEQYRFVMPGAALNEDEFRQLEEQVLEIESGAILVISGSLPPGVKLEKLTQLISAAQKQGIRCIVDSSGEALSAALAIGNIELVKPNQKELSALVNRELTQPDDVRKAAQEIVNSGKAKRVVVSLGPQGALGVDSENCIQVVPPPVKSQSTVGAGDSMVGAMTLKLAENASLEEMVRFGVAAGSAATLNQGTRLCSHDDTQKIYAYLSR 309
               SCOP domains d3umob_ B: automated matches                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....eeeeeeee.......eee....eeeeehhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhhh...eeeee........eeeee.....eeeee......hhhhhhhhhhhhh......eeeee.......hhhhhhhhhhhhhhh..eeeee.hhhhhhhhh......ee..hhhhhhhhhh......hhhhhhhhhhhhh.....eeee.hhh.eeee....eeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------PFKB_KINASES_1           -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2---------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3umo B   1 MVRIYTLTLAPSLDSATITPQIYPEGKLRCTAPVFEPGGGGINVARAIAHLGGSATAIFPAGGATGEHLVSLLADENVPVATVEAKDWTRQNLHVHVEASGEQYRFVMPGAALNEDEFRQLEEQVLEIESGAILVISGSLPPGVKLEKLTQLISAAQKQGIRCIVDSSGEALSAALAIGNIELVKPNQKELSALVNRELTQPDDVRKAAQEIVNSGKAKRVVVSLGPQGALGVDSENCIQVVPPPVKSQSTVGAGDSMVGAMTLKLAENASLEEMVRFGVAAGSAATLNQGTRLCSHDDTQKIYAYLSR 309
                                    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         

   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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PFKB_ECOLI | P06999)
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: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:0016773    phosphotransferase activity, alcohol group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
    GO:0009024    tagatose-6-phosphate kinase activity    Catalysis of the reaction: ATP + D-tagatose 6-phosphate = ADP + D-tagatose 1,6-bisphosphate.
    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: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:0006974    cellular response to DNA damage stimulus    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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PFKB_ECOLI | P069993cqd 3n1c 3ump 3uqd 3uqe

(-) Related Entries Specified in the PDB File

3cqd 3ump