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(-) Description

Title :  CRYSTAL STRUCTURE OF PYROPHOSPHATE-DEPENDENT PHOSPHOFRUCTOKINASE FROM MARINOBACTER AQUAEOLEI, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET MQR88
 
Authors :  J. Seetharaman, S. Lew, D. Wang, H. Neely, K. Janjua, K. Cunningham, L. Owens, R. Xiao, J. Liu, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  30 Sep 09  (Deposition) - 17 Nov 09  (Release) - 17 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Pyrophosphate-Dependent Phosphofructokinase, Kinase Transferase, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Seetharaman, S. Lew, D. Wang, H. Neely, K. Janjua, K. Cunningham, L. Owens, R. Xiao, J. Liu, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt, L. Tong
Crystal Structure Of Pyrophosphate-Dependent Phosphofructokinase From Marinobacter Aquaeolei, Northeast Structural Genomics Consortium Target Mqr88
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PYROPHOSPHATE-DEPENDENT PHOSPHOFRUCTOKINASE
    Chains: A, B, C
    EC Number: 2.7.1.90
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MAQU_2402
    Organism Common: MARINOBACTER HYDROCARBONOCLASTICUS (STRAIN DSM 11845)
    Organism Scientific: MARINOBACTER AQUAEOLEI VT8
    Organism Taxid: 351348
    Strain: ATCC 700491 / DSM 11845 / VT8

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): A  
Biological Unit 2 (1x):  BC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1NA3Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:80 , HOH A:438BINDING SITE FOR RESIDUE NA A 421
2AC2SOFTWAREARG B:80BINDING SITE FOR RESIDUE NA B 421
3AC3SOFTWAREARG C:80 , HOH C:526BINDING SITE FOR RESIDUE NA C 421

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K2Q)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Pro A:211 -Pro A:212
2Pro B:211 -Pro B:212
3Pro C:211 -Pro C:212

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K2Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K2Q)

(-) Exons   (0, 0)

(no "Exon" information available for 3K2Q)

(-) 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:392
 aligned with A1U3A9_MARHV | A1U3A9 from UniProtKB/TrEMBL  Length:420

    Alignment length:418
                                    12        22        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        
         A1U3A9_MARHV     3 IKNAFYAQSGGVTAVINASACGVIQTARKHPDQIGKVYAGRNGIIGALKEELIDTSLESDDAIQALIHTPGGAFGSCRYKLKNISENQREYERLIEVFRAHDIGYFFYNGGGDSQDTAYKVSQLADRMGYPITCIGVPKTVDNDLPFTDCCPGFGSVAKYIATSTLEASLDIKSMCETSTKVFILEVMGRHAGWIAAAGGLAGQSEGEPPHVILFPEIPFNREKFLERVDQCVRDYGYCVVVASEGAQYEDGRFVADAGAKDAFGHTQLGGVAPALANMVKQALGHKYHWAVADYLQRAARHIASATDVEQAYAVGKAAVEMALAGKQALMPTIVRDQAKPYRWSIGEANLSEVANQEKKMPIHYITDNGFGITQDCRDYLQPLIAGESFPPFDDGLPRVAKLKNQLVEKKLRTEFEL 420
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhh........eeee..hhhhhhh..eee.hhhhhhhhhhhhhh...........--------hhhhhhhhhhhhh.eeeeeeeehhhhhhhhhhhhhhhhhh....eeeeee..............hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhh........eee......hhhhhhhhhhhhhh....eeeeee......--..----------------.hhhhhhhhhhhhhh..eeeee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee....eeeeeeeehhhhh......hhhhh.......hhhhhhhhhhhhh......ee..ee.................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k2q A   3 IKNAFYAQSGGVTAVINASACGVIQTARKHPDQIGKVYAGRNGIIGALKEELIDTSLESDDAIQALIHTPGGAFGSCRYK--------REYERLIEVFRAHDIGYFFYNGGGDSQDTAYKVSQLADRMGYPITCIGVPKTVDNDLPFTDCCPGFGSVAKYIATSTLEASLDIKSMCETSTKVFILEVMGRHAGWIAAAGGLAGQSEGEPPHVILFPEIPFNREKFLERVDQCVRDYGYCVVVASEGAQYE--RF----------------GVAPALANMVKQALGHKYHWAVADYLQRAARHIASATDVEQAYAVGKAAVEMALAGKQALMPTIVRDQAKPYRWSIGEANLSEVANQEKKMPIHYITDNGFGITQDCRDYLQPLIAGESFPPFDDGLPRVAKLKNQLVEKKLRTEFEL 420
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252  ||     -         -|      282       292       302       312       322       332       342       352       362       372       382       392       402       412        
                                                                                                          82       91                                                                                                                                                              252  ||              273                                                                                                                                                   
                                                                                                                                                                                                                                                                                      255|                                                                                                                                                                    
                                                                                                                                                                                                                                                                                       256                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:392
 aligned with A1U3A9_MARHV | A1U3A9 from UniProtKB/TrEMBL  Length:420

    Alignment length:418
                                    12        22        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        
         A1U3A9_MARHV     3 IKNAFYAQSGGVTAVINASACGVIQTARKHPDQIGKVYAGRNGIIGALKEELIDTSLESDDAIQALIHTPGGAFGSCRYKLKNISENQREYERLIEVFRAHDIGYFFYNGGGDSQDTAYKVSQLADRMGYPITCIGVPKTVDNDLPFTDCCPGFGSVAKYIATSTLEASLDIKSMCETSTKVFILEVMGRHAGWIAAAGGLAGQSEGEPPHVILFPEIPFNREKFLERVDQCVRDYGYCVVVASEGAQYEDGRFVADAGAKDAFGHTQLGGVAPALANMVKQALGHKYHWAVADYLQRAARHIASATDVEQAYAVGKAAVEMALAGKQALMPTIVRDQAKPYRWSIGEANLSEVANQEKKMPIHYITDNGFGITQDCRDYLQPLIAGESFPPFDDGLPRVAKLKNQLVEKKLRTEFEL 420
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhhh.......eeee..hhhhhhh..eee.hhhhhhhhhhhhhh...........--------hhhhhhhhhhhhh.eeeeeeeehhhhhhhhhhhhhhhhhh....eeeeee..............hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhh........eee......hhhhhhhhhhhhhh....eeeeee......--..----------------hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee....eeeeeeeehhhhh......hhhhh.......hhhhhhhhhhhhh................................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k2q B   3 IKNAFYAQSGGVTAVINASACGVIQTARKHPDQIGKVYAGRNGIIGALKEELIDTSLESDDAIQALIHTPGGAFGSCRYK--------REYERLIEVFRAHDIGYFFYNGGGDSQDTAYKVSQLADRMGYPITCIGVPKTVDNDLPFTDCCPGFGSVAKYIATSTLEASLDIKSMCETSTKVFILEVMGRHAGWIAAAGGLAGQSEGEPPHVILFPEIPFNREKFLERVDQCVRDYGYCVVVASEGAQYE--RF----------------GVAPALANMVKQALGHKYHWAVADYLQRAARHIASATDVEQAYAVGKAAVEMALAGKQALMPTIVRDQAKPYRWSIGEANLSEVANQEKKMPIHYITDNGFGITQDCRDYLQPLIAGESFPPFDDGLPRVAKLKNQLVEKKLRTEFEL 420
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252  ||     -         -|      282       292       302       312       322       332       342       352       362       372       382       392       402       412        
                                                                                                          82       91                                                                                                                                                              252  ||              273                                                                                                                                                   
                                                                                                                                                                                                                                                                                      255|                                                                                                                                                                    
                                                                                                                                                                                                                                                                                       256                                                                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:392
 aligned with A1U3A9_MARHV | A1U3A9 from UniProtKB/TrEMBL  Length:420

    Alignment length:418
                                    12        22        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        
         A1U3A9_MARHV     3 IKNAFYAQSGGVTAVINASACGVIQTARKHPDQIGKVYAGRNGIIGALKEELIDTSLESDDAIQALIHTPGGAFGSCRYKLKNISENQREYERLIEVFRAHDIGYFFYNGGGDSQDTAYKVSQLADRMGYPITCIGVPKTVDNDLPFTDCCPGFGSVAKYIATSTLEASLDIKSMCETSTKVFILEVMGRHAGWIAAAGGLAGQSEGEPPHVILFPEIPFNREKFLERVDQCVRDYGYCVVVASEGAQYEDGRFVADAGAKDAFGHTQLGGVAPALANMVKQALGHKYHWAVADYLQRAARHIASATDVEQAYAVGKAAVEMALAGKQALMPTIVRDQAKPYRWSIGEANLSEVANQEKKMPIHYITDNGFGITQDCRDYLQPLIAGESFPPFDDGLPRVAKLKNQLVEKKLRTEFEL 420
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......hhhhhhhhhhhhhh.....eeeeeee..hhhhhhh..eee.hhhhhhhhhhhhhh...........--------hhhhhhhhhhhhh.eeeeeeeehhhhhhhhhhhhhhhhhh....eeeeee..............hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhh........eee......hhhhhhhhhhhhhh....eeeeee......--..----------------hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee....eeeeeeeehhhhh......hhhhh.......hhhhhhhhh..........ee..ee.................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k2q C   3 IKNAFYAQSGGVTAVINASACGVIQTARKHPDQIGKVYAGRNGIIGALKEELIDTSLESDDAIQALIHTPGGAFGSCRYK--------REYERLIEVFRAHDIGYFFYNGGGDSQDTAYKVSQLADRMGYPITCIGVPKTVDNDLPFTDCCPGFGSVAKYIATSTLEASLDIKSMCETSTKVFILEVMGRHAGWIAAAGGLAGQSEGEPPHVILFPEIPFNREKFLERVDQCVRDYGYCVVVASEGAQYE--RF----------------GVAPALANMVKQALGHKYHWAVADYLQRAARHIASATDVEQAYAVGKAAVEMALAGKQALMPTIVRDQAKPYRWSIGEANLSEVANQEKKMPIHYITDNGFGITQDCRDYLQPLIAGESFPPFDDGLPRVAKLKNQLVEKKLRTEFEL 420
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252  ||     -         -|      282       292       302       312       322       332       342       352       362       372       382       392       402       412        
                                                                                                          82       91                                                                                                                                                              252  ||              273                                                                                                                                                   
                                                                                                                                                                                                                                                                                      255|                                                                                                                                                                    
                                                                                                                                                                                                                                                                                       256
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3K2Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K2Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3K2Q)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (A1U3A9_MARHV | A1U3A9)
molecular function
    GO:0003872    6-phosphofructokinase activity    Catalysis of the reaction: ATP + D-fructose-6-phosphate = ADP + D-fructose 1,6-bisphosphate.
    GO:0047334    diphosphate-fructose-6-phosphate 1-phosphotransferase activity    Catalysis of the reaction: fructose-6-phosphate + diphosphate = phosphate + fructose-1,6-bisphosphate.
    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: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: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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