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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FRUCTOSE-1,6-BISPHOSPHATASE GLPX FROM E.COLI IN COMPLEX WITH INORGANIC PHOSPHATE
 
Authors :  V. V. Lunin, T. Skarina, G. Brown, A. F. Yakunin, A. M. Edwards, A. Savche
Date :  30 Nov 07  (Deposition) - 09 Dec 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Glpx, 1, 6-Bisphosphatase, Carbohydrate Metabolism, Hydrolase, Manganese (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Brown, A. Singer, V. V. Lunin, M. Proudfoot, T. Skarina, R. Flick, S. Kochinyan, R. Sanishvili, A. Joachimiak, A. M. Edwards, A. Savchenko, A. F. Yakunin
Structural And Biochemical Characterization Of The Type Ii Fructose-1, 6-Bisphosphatase Glpx From Escherichia Coli.
J. Biol. Chem. V. 284 3784 2009
PubMed-ID: 19073594  |  Reference-DOI: 10.1074/JBC.M808186200

(-) Compounds

Molecule 1 - FRUCTOSE-1,6-BISPHOSPHATASE CLASS II GLPX
    Chains: A
    EC Number: 3.1.3.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GLPX, B3925, JW3896
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Strain: K12
    Synonym: D-FRUCTOSE-1,6-BISPHOSPHATE 1-PHOSPHOHYDROLASE CLASS II GLPX, FBPASE II GLPX

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
2UNX1Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:119 , LYS A:164 , ARG A:166 , LYS A:239BINDING SITE FOR RESIDUE PO4 A 401
2AC2SOFTWAREASP A:85 , ILE A:87 , HOH A:437 , HOH A:487 , HOH A:539 , HOH A:540BINDING SITE FOR RESIDUE UNX A 400

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BIG)

(-) 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:321
 aligned with GLPX_ECOLI | P0A9C9 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:324
                                    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       320    
           GLPX_ECOLI     1 MRRELAIEFSRVTESAALAGYKWLGRGDKNTADGAAVNAMRIMLNQVNIDGTIVIGEGEIDEAPMLYIGEKVGTGRGDAVDIAVDPIEGTRMTAMGQANALAVLAVGDKGCFLNAPDMYMEKLIVGPGAKGTIDLNLPLADNLRNVAAALGKPLSELTVTILAKPRHDAVIAEMQQLGVRVFAIPDGDVAASILTCMPDSEVDVLYGIGGAPEGVVSAAVIRALDGDMNGRLLARHDVKGDNEENRRIGEQELARCKAMGIEAGKVLRLGDMARSDNVIFSATGITKGDLLEGISRKGNIATTETLLIRGKSRTIRRIQSIHYL 324
               SCOP domains d3biga_ A: automated matches                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 3bigA01 A:1-109,A:277-324 Fructose-1,6-Bisphosphatase, subunit A, domain 1                                   3bigA02 A:110-276  [code=3.40.190.90, no name defined]                                                                                                                 3bigA01 A:1-109,A:277-324                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....eeeeee...............ee......eeeeeeeeeehhhhhhh.....eeeeeeee..........eeeeeee.hhhh.......hhhhhhhhhhhhhh.hhhh.eeeee.hhhhhhhhhhhhhhh.eeeee...hhhhhhhh........eeeeeeehhhhhhhhhhhhhhh.eeeeeeehhhhh.--.hhhhhhhhhhhhhhhh.......eeehhhhh....eeeeeee..........eee..eeeeeeeeee...-.eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3big A   1 MRRELAIEFSRVTESAALAGYKWLGRGDKNTADGAAVNAMRIMLNQVNIDGTIVIGEGEIAEAPMLYIGEKVGTGRGDAVDIAVDPIEGTRMTAMGQANALAVLAVGDKGCFLNAPDMYMEKLIVGPGAKGTIDLNLPLADNLRNVAAALGKPLSELTVTILAKPRHDAVIAEMQQLGVRVFAIPDGDVAASILTCMPDSEVDVLYGIGGAPEGVVSAAVIRALDGDMNGRLLARHDVK--NEENRRIGEQELARCKAMGIEAGKVLRLGDMARSDNVIFSATGITKGDLLEGISRKGNIATTETLLIRGKS-TIRRIQSIHYL 324
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        |- |     250       260       270       280       290       300       310 | |   320    
                                                                                                                                                                                                                                                                        239  |                                                                   312 |          
                                                                                                                                                                                                                                                                           242                                                                     314
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GLPX_ECOLI | P0A9C9)
molecular function
    GO:0042132    fructose 1,6-bisphosphate 1-phosphatase activity    Catalysis of the reaction: D-fructose 1,6-bisphosphate + H2O = D-fructose 6-phosphate + phosphate.
    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:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    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:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0006094    gluconeogenesis    The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
    GO:0006071    glycerol metabolic process    The chemical reactions and pathways involving glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
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

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UniProtKB/Swiss-Prot
        GLPX_ECOLI | P0A9C9: 1ni9 2r8t 3bih 3d1r

(-) Related Entries Specified in the PDB File

3bih CRYSTAL STRUCTURE OF FRUCTOSE-1,6-BISPHOSPHATASE FROM E.COLI GLPX