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(-) Description

Title :  CRYSTAL STRUCTURE OF 6-PHOSPHOGLUCONOLACTONASE FROM TRYPANOSOMA BRUCEI COMPLEXED WITH 6-PHOSPHOGLUCONIC ACID
 
Authors :  L. Poggi, M. Delarue, N. Duclert-Savatier, V. Stoven
Date :  18 Aug 08  (Deposition) - 26 May 09  (Release) - 26 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Catalytic Mechanism, Pentose Phosphate Pathway, 6- Phosphogluconolactonase, Trypanosoma Brucei, Hydrolase, Zinc Binding Site (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Duclert-Savatier, L. Poggi, E. Miclet, P. Lopes, J. Ouazzani, N. Chevalier, M. Nilges, M. Delarue, V. Stoven
Insights Into The Enzymatic Mechanism Of 6-Phosphogluconolactonase From Trypanosoma Brucei Using Structural Data And Molecular Dynamics Simulation.
J. Mol. Biol. V. 388 1009 2009
PubMed-ID: 19345229  |  Reference-DOI: 10.1016/J.JMB.2009.03.063
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 6-PHOSPHOGLUCONOLACTONASE
    Chains: A, B
    EC Number: 3.1.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 6PGL
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
16PG2Ligand/Ion6-PHOSPHOGLUCONIC ACID
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
16PG1Ligand/Ion6-PHOSPHOGLUCONIC ACID
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
16PG1Ligand/Ion6-PHOSPHOGLUCONIC ACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:56 , HIS A:97 , ASP A:98 , HOH A:340BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWARESER A:46 , THR A:47 , ARG A:77 , HIS A:165 , MET A:194 , LYS A:195 , ARG A:200 , LYS A:223 , HOH A:298 , HOH A:334 , HOH A:394BINDING SITE FOR RESIDUE 6PG A 843
3AC3SOFTWAREHIS B:56 , HIS B:97 , ASP B:98 , HOH B:408BINDING SITE FOR RESIDUE ZN B 300
4AC4SOFTWARESER B:46 , THR B:47 , ARG B:77 , GLY B:159 , LEU B:160 , HIS B:165 , MET B:194 , LYS B:195 , ARG B:200 , LYS B:223 , HOH B:340 , HOH B:341 , HOH B:374 , HOH B:465BINDING SITE FOR RESIDUE 6PG B 843

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E7F)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Trp A:36 -Pro A:37
2Lys A:195 -Pro A:196
3Trp B:36 -Pro B:37
4Lys B:195 -Pro B:196

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E7F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3E7F)

(-) Exons   (0, 0)

(no "Exon" information available for 3E7F)

(-) 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:260
 aligned with Q9GRG6_9TRYP | Q9GRG6 from UniProtKB/TrEMBL  Length:266

    Alignment length:260
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261
         Q9GRG6_9TRYP     2 SFKPTISVHATPQELSAAGCRKIVEIIEASGSQQWPLSIALAGGSTPKMTYARLHDEHLNLLREKRALRFFMGDERMVPADSTDSNYNMAREVLLHDIPDDLVFPFDTSAVTPSAEATSADAMRVAEAYGKQLASLLPLKSVGEAGPKVPVFDVVLLGLGSDGHTASIFPGSQAEKETDGKVVVSVGFPSETMKPKVWRVTLSPATIMQARNVIVLATGAEKKWVVDGILADTAHKAPVARFLRGCEGNVSFLLDKEIAE 261
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhhh....eeeee.eee........hhhhhhhhhhhhhhhhh.ee.............hhhhhhhhhhhhhhhhhhhh.eee......eee...eeee...............hhhhh......eeee...........eeeehhhhhhhh.eeeeee.hhhhhhhhhhhhh......hhhhhhhhh..eeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e7f A   2 SFKPTISVHATPQELSAAGCRKIVEIIEASGSQQWPLSIALAGGSTPKMTYARLHDEHLNLLREKRALRFFMGDERMVPADSTDSNYNMAREVLLHDIPDDLVFPFDTSAVTPSAEATSADAMRVAEAYGKQLASLLPLKSVGEAGPKVPVFDVVLLGLGSDGHTASIFPGSQAEKETDGKVVVSVGFPSETMKPKVWRVTLSPATIMQARNVIVLATGAEKKWVVDGILADTAHKAPVARFLRGCEGNVSFLLDKEIAE 261
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261


Chain B from PDB  Type:PROTEIN  Length:263
 aligned with Q9GRG6_9TRYP | Q9GRG6 from UniProtKB/TrEMBL  Length:266

    Alignment length:263
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261   
         Q9GRG6_9TRYP     2 SFKPTISVHATPQELSAAGCRKIVEIIEASGSQQWPLSIALAGGSTPKMTYARLHDEHLNLLREKRALRFFMGDERMVPADSTDSNYNMAREVLLHDIPDDLVFPFDTSAVTPSAEATSADAMRVAEAYGKQLASLLPLKSVGEAGPKVPVFDVVLLGLGSDGHTASIFPGSQAEKETDGKVVVSVGFPSETMKPKVWRVTLSPATIMQARNVIVLATGAEKKWVVDGILADTAHKAPVARFLRGCEGNVSFLLDKEIAENLA 264
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhhh....eeeee.eee........hhhhhhhhhhhhhhhhh.ee.............hhhhhhhhhhhhhhhhhhhh.eee......eee...eeee...............hhhhh......eeee...........eeeehhhhhhhh.eeeeee.hhhhhhhhhhhhh......hhhhhhhhh..eeeeeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e7f B   2 SFKPTISVHATPQELSAAGCRKIVEIIEASGSQQWPLSIALAGGSTPKMTYARLHDEHLNLLREKRALRFFMGDERMVPADSTDSNYNMAREVLLHDIPDDLVFPFDTSAVTPSAEATSADAMRVAEAYGKQLASLLPLKSVGEAGPKVPVFDVVLLGLGSDGHTASIFPGSQAEKETDGKVVVSVGFPSETMKPKVWRVTLSPATIMQARNVIVLATGAEKKWVVDGILADTAHKAPVARFLRGCEGNVSFLLDKEIAENLA 264
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261
   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  (0, 0)

(no "SCOP Domain" information available for 3E7F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3E7F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E7F)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9GRG6_9TRYP | Q9GRG6)
molecular function
    GO:0017057    6-phosphogluconolactonase activity    Catalysis of the reaction: 6-O-phosphono-D-glucono-1,5-lactone + H(2)O = 6-phospho-D-gluconate + H(+).
    GO:0004341    gluconolactonase activity    Catalysis of the reaction: D-glucono-1,5-lactone + H2O = D-gluconate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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:0006098    pentose-phosphate shunt    The glucose-6-phosphate catabolic process in which, coupled to NADPH synthesis, glucose-6-P is oxidized with the formation of carbon dioxide (CO2) and ribulose 5-phosphate; ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0020015    glycosome    A membrane-bounded organelle found in organisms from the order Kinetoplastida that houses the enzymes of glycolysis.

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        Q9GRG6_9TRYP | Q9GRG6: 2j0e 3eb9

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2j0e