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(-) Description

Title :  CLASS II FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE FROM HELICOBACTER PYLORI IN COMPLEX WITH N-(4-HYDROXYBUTYL)- GLYCOLOHYDROXAMIC ACID BIS-PHOSPHATE, A COMPETITIVE INHIBITOR
 
Authors :  M. Coincon, S. Sygusch
Date :  31 May 10  (Deposition) - 17 Nov 10  (Release) - 08 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fbp Aldolase, Class Ii, Inhibitor, Lyase, Lyase-Lyase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Daher, M. Fonvielle, P. M. Gest, M. E. Guerin, M. Jackson, J. Sygusch M. Therisod
Rational Design, Synthesis, And Evaluation Of New Selective Inhibitors Of Microbial Class Ii (Zinc Dependent) Fructose Bis-Phosphate Aldolases.
J. Med. Chem. V. 53 7836 2010
PubMed-ID: 20929256  |  Reference-DOI: 10.1021/JM1009814

(-) Compounds

Molecule 1 - FRUCTOSE-BISPHOSPHATE ALDOLASE
    Chains: A, B
    EC Number: 4.1.2.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK233-3
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ALF_HELPY
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 290847
    Strain: 51

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2NA2Ligand/IonSODIUM ION
3TD42Ligand/Ion4-{HYDROXY[(PHOSPHONOOXY)ACETYL]AMINO}BUTYL DIHYDROGENPHOSPHATE
4ZN2Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:23 , SER A:49 , ASP A:82 , HIS A:83 , HIS A:180 , GLY A:181 , LYS A:184 , HIS A:210 , GLY A:211 , ALA A:212 , SER A:213 , ASN A:253 , ASP A:255 , THR A:256 , ZN A:309 , HOH A:345 , HOH A:399 , HOH A:450 , HOH A:464 , HOH A:587 , HOH A:611 , HOH A:644 , HOH A:849 , ARG B:280BINDING SITE FOR RESIDUE TD4 A 308
2AC2SOFTWAREHIS A:83 , HIS A:180 , HIS A:210 , TD4 A:308BINDING SITE FOR RESIDUE ZN A 309
3AC3SOFTWAREASP A:104 , SER A:106 , GLU A:134 , HOH A:320 , HOH A:449 , HOH A:638BINDING SITE FOR RESIDUE CA A 310
4AC4SOFTWAREHIS A:80 , ASP A:82 , MET A:102 , GLU A:132 , HIS A:210 , LYS A:251 , ASN A:253BINDING SITE FOR RESIDUE NA A 311
5AC5SOFTWAREHIS B:83 , HIS B:180 , HIS B:210 , TD4 B:311BINDING SITE FOR RESIDUE ZN B 308
6AC6SOFTWAREASP B:104 , SER B:106 , GLU B:134 , HOH B:349 , HOH B:351 , HOH B:436BINDING SITE FOR RESIDUE CA B 309
7AC7SOFTWAREHIS B:80 , ASP B:82 , MET B:102 , GLU B:132 , HIS B:210 , LYS B:251 , ASN B:253BINDING SITE FOR RESIDUE NA B 310
8AC8SOFTWAREARG A:280 , ASN B:23 , SER B:49 , ASP B:82 , HIS B:83 , HIS B:180 , GLY B:181 , LYS B:184 , HIS B:210 , GLY B:211 , ALA B:212 , SER B:213 , ASN B:253 , ASP B:255 , THR B:256 , ZN B:308 , HOH B:325 , HOH B:347 , HOH B:389 , HOH B:416 , HOH B:450 , HOH B:513 , HOH B:991 , HOH B:992BINDING SITE FOR RESIDUE TD4 B 311

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N9S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3N9S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N9S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3N9S)

(-) Exons   (0, 0)

(no "Exon" information available for 3N9S)

(-) Sequences/Alignments

Asymmetric/Biological 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:307
 aligned with D0IR47_HELP1 | D0IR47 from UniProtKB/TrEMBL  Length:307

    Alignment length:307
                                    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       
         D0IR47_HELP1     1 MLVKGNEILLKAHKEGYGVGAFNFVNFEMLNAIFEAGNEENSPLFIQASEGAIKYMGIDMAVGMVKIMCERYPHIPVALHLDHGTTFESCEKAVKAGFTSVMIDASHHAFEENLELTSKVVKMAHNAGVSVEAELGRLMGIEDNISVDEKDAVLVNPKEAEQFVKESQVDYLAPAIGTSHGAFKFKGEPKLDFERLQEVKRLTNIPLVLHGASAIPDDVRKSYLDAGGDLKGSKGVPFEFLQESVKGGINKVNTDTDLRIAFIAEVRKVANEDKSQFDLRKFFSPAQLALKNVVKERMKLLGSANKI 307
               SCOP domains d3n9sa_ A: automated matches                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhh..eeeeee....................hhhhhhhhhhhhh..eeee.................hhhhhhhhhhhhh..eee......hhhhhhhhhhh..........hhhhhhhhhhhheeeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n9s A   1 MLVKGNEILLKAHKEGYGVGAFNFVNFEMLNAIFEAGNEENSPLFIQASEGAIKYMGIDMAVGMVKIMCERYPHIPVALHLDHGTTFESCEKAVKAGFTSVMIDASHHAFEENLELTSKVVKMAHNAGVSVEAELGRLMGIEDNISVDEKDAVLVNPKEAEQFVKESQVDYLAPAIGTSHGAFKFKGEPKLDFERLQEVKRLTNIPLVLHGASAIPDNVRKSYLDAGGDLKGSKGVPFEFLQESVKGGINKVNTDTDLRIAFIAEVRKVANEDKSQFDLRKFFSPAQLALKNVVKERMKLLGSANKI 307
                                    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:295
 aligned with D0IR47_HELP1 | D0IR47 from UniProtKB/TrEMBL  Length:307

    Alignment length:307
                                    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       
         D0IR47_HELP1     1 MLVKGNEILLKAHKEGYGVGAFNFVNFEMLNAIFEAGNEENSPLFIQASEGAIKYMGIDMAVGMVKIMCERYPHIPVALHLDHGTTFESCEKAVKAGFTSVMIDASHHAFEENLELTSKVVKMAHNAGVSVEAELGRLMGIEDNISVDEKDAVLVNPKEAEQFVKESQVDYLAPAIGTSHGAFKFKGEPKLDFERLQEVKRLTNIPLVLHGASAIPDDVRKSYLDAGGDLKGSKGVPFEFLQESVKGGINKVNTDTDLRIAFIAEVRKVANEDKSQFDLRKFFSPAQLALKNVVKERMKLLGSANKI 307
               SCOP domains d3n9sb_ B: automated matches                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) F_bP_aldolase-3n9sB01 B:1-307                                                                                                                                                                                                                                                                                       Pfam domains (1)
           Pfam domains (2) F_bP_aldolase-3n9sB02 B:1-307                                                                                                                                                                                                                                                                                       Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhh..eeeeee....------------....hhhhhhhhhhhhh..eeee.................hhhhhhhhhhhhh..eee......hhhhhhhhhhh..........hhhhhhhhhhhheeeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n9s B   1 MLVKGNEILLKAHKEGYGVGAFNFVNFEMLNAIFEAGNEENSPLFIQASEGAIKYMGIDMAVGMVKIMCERYPHIPVALHLDHGTTFESCEKAVKAGFTSVMIDASHHAFEENLELTSKVVKMAHNAGVSVEAELGRLM------------AVLVNPKEAEQFVKESQVDYLAPAIGTSHGAFKFKGEPKLDFERLQEVKRLTNIPLVLHGASAIPDNVRKSYLDAGGDLKGSKGVPFEFLQESVKGGINKVNTDTDLRIAFIAEVRKVANEDKSQFDLRKFFSPAQLALKNVVKERMKLLGSANKI 307
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        |-         - |     160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       
                                                                                                                                                                    139          152
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N9S)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (D0IR47_HELP1 | D0IR47)
molecular function
    GO:0016832    aldehyde-lyase activity    Catalysis of the cleavage of a C-C bond in a molecule containing a hydroxyl group and a carbonyl group to form two smaller molecules, each being an aldehyde or a ketone.
    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:0004332    fructose-bisphosphate aldolase activity    Catalysis of the reaction: D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde-3-phosphate.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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:0030388    fructose 1,6-bisphosphate metabolic process    The chemical reactions and pathways involving fructose 1,6-bisphosphate, also known as FBP. The D enantiomer is a metabolic intermediate in glycolysis and gluconeogenesis.
    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.

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 Related Entries

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

UniProtKB/TrEMBL
        D0IR47_HELP1 | D0IR47: 3n9r

(-) Related Entries Specified in the PDB File

3c4u 3c52 3c56 3n9r