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(-) Description

Title :  CRYSTAL STRUCTURE OF PFK FROM BACILLUS SUBTILIS
 
Authors :  J. A. Newman, L. Hewitt, C. Rodrigues, A. S. Solovyova, C. R. Harwood, R.
Date :  04 Oct 11  (Deposition) - 15 Aug 12  (Release) - 03 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (2x),B (2x)
Biol. Unit 2:  A (2x),B (2x)
Keywords :  Transferase, Glycolysis, Degradosome (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. A. Newman, L. Hewitt, C. Rodrigues, A. S. Solovyova, C. R. Harwood, R. J. Lewis
Dissection Of The Network Of Interactions That Links Rna Processing With Glycolysis In The Bacillus Subtilis Degradosome.
J. Mol. Biol. V. 416 121 2012
PubMed-ID: 22198292  |  Reference-DOI: 10.1016/J.JMB.2011.12.024

(-) Compounds

Molecule 1 - 6-PHOSPHOFRUCTOKINASE
    ChainsA, B
    EC Number2.7.1.11
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423
    Strain168
    SynonymPHOSPHOFRUCTOKINASE, PHOSPHOHEXOKINASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4A3S)

(-) Sites  (0, 0)

(no "Site" information available for 4A3S)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4A3S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4A3S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4A3S)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PHOSPHOFRUCTOKINASEPS00433 Phosphofructokinase signature.PFKA_BACSU243-261
 
  2A:243-261
B:243-261
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PHOSPHOFRUCTOKINASEPS00433 Phosphofructokinase signature.PFKA_BACSU243-261
 
  4A:243-261
B:243-261
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PHOSPHOFRUCTOKINASEPS00433 Phosphofructokinase signature.PFKA_BACSU243-261
 
  4A:243-261
B:243-261

(-) Exons   (0, 0)

(no "Exon" information available for 4A3S)

(-) 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:319
 aligned with PFKA_BACSU | O34529 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:319
                                    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         
           PFKA_BACSU     1 MKRIGVLTSGGDSPGMNAAVRAVVRKAIYHDVEVYGIYNGYAGLISGKIEKLELGSVGDIIHRGGTKLYTARCPEFKTVEGREKGIANLKKLGIEGLVVIGGDGSYMGAKKLTEHGFPCVGVPGTIDNDIPGTDFTIGFDTALNTVIDAIDKIRDTATSHERTYVIEVMGRHAGDIALWAGLAGGAESILIPEADYDMHEIIARLKRGHERGKKHSIIIVAEGVGSGVEFGKRIEEETNLETRVSVLGHIQRGGSPSAADRVLASRLGAYAVELLLEGKGGRCVGIQNNKLVDHDIIEILETKHTVEQNMYQLSKELSI 319
               SCOP domains d4a3sa_ A: automated matches                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhhhhh..eeeee...hhhhhhh.eeeehhhhhh..............hhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhh...eeeeeee...........eehhhhhhhhhhhhhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhh..eee......hhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhh..eeeee.hhhhhh...hhhhhhhhhhhhhhhhhhhh.....eeeeee..eeeeeehhhhh......hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PHOSPHOFRUCTOKINASE---------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a3s A   1 MKRIGVLTSGGDSPGMNAAVRAVVRKAIYHDVEVYGIYNGYAGLISGKIEKLELGSVGDIIHRGGTKLYTARCPEFKTVEGREKGIANLKKLGIEGLVVIGGDGSYMGAKKLTEHGFPCVGVPGTIDNDIPGTDFTIGFDTALNTVIDAIDKIRDTATSHERTYVIEVMGRHAGDIALWAGLAGGAESILIPEADYDMHEIIARLKRGHERGKKHSIIIVAEGVGSGVEFGKRIEEETNLETRVSVLGHIQRGGSPSAADRVLASRLGAYAVELLLEGKGGRCVGIQNNKLVDHDIIEILETKHTVEQNMYQLSKELSI 319
                                    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         

Chain B from PDB  Type:PROTEIN  Length:319
 aligned with PFKA_BACSU | O34529 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:319
                                    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         
           PFKA_BACSU     1 MKRIGVLTSGGDSPGMNAAVRAVVRKAIYHDVEVYGIYNGYAGLISGKIEKLELGSVGDIIHRGGTKLYTARCPEFKTVEGREKGIANLKKLGIEGLVVIGGDGSYMGAKKLTEHGFPCVGVPGTIDNDIPGTDFTIGFDTALNTVIDAIDKIRDTATSHERTYVIEVMGRHAGDIALWAGLAGGAESILIPEADYDMHEIIARLKRGHERGKKHSIIIVAEGVGSGVEFGKRIEEETNLETRVSVLGHIQRGGSPSAADRVLASRLGAYAVELLLEGKGGRCVGIQNNKLVDHDIIEILETKHTVEQNMYQLSKELSI 319
               SCOP domains d4a3sb_ B: automated matches                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhhhhh..eeeee...hhhhhhh.eee.hhhhhh..............hhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhh...eeeeeee...........eehhhhhhhhhhhhhhhhhhhhhhh.eeeeee.....hhhhhhhhhhh...eee......hhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhh..eeeee.hhhhhh...hhhhhhhhhhhhhhhhhhhh.....eeeeee..eeeeee.hhhh......hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PHOSPHOFRUCTOKINASE---------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a3s B   1 MKRIGVLTSGGDSPGMNAAVRAVVRKAIYHDVEVYGIYNGYAGLISGKIEKLELGSVGDIIHRGGTKLYTARCPEFKTVEGREKGIANLKKLGIEGLVVIGGDGSYMGAKKLTEHGFPCVGVPGTIDNDIPGTDFTIGFDTALNTVIDAIDKIRDTATSHERTYVIEVMGRHAGDIALWAGLAGGAESILIPEADYDMHEIIARLKRGHERGKKHSIIIVAEGVGSGVEFGKRIEEETNLETRVSVLGHIQRGGSPSAADRVLASRLGAYAVELLLEGKGGRCVGIQNNKLVDHDIIEILETKHTVEQNMYQLSKELSI 319
                                    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         

   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 4A3S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A3S)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PFKA_BACSU | O34529)
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: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:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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: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: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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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(-) Related Entries Specified in the PDB File

4a3r CRYSTAL STRUCTURE OF ENOLASE FROM BACILLUS SUBTILIS.