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(-) Description

Title :  CRYSTAL STRUCTURE OF CALCIUM-BOUND D,D-HEPTOSE 1.7-BISPHOSPHATE PHOSPHATASE FROM E. COLI
 
Authors :  S. N. Sugiman-Marangos, M. S. Junop
Date :  06 Oct 08  (Deposition) - 14 Oct 08  (Release) - 11 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Carbohydrate Metabolism, Hydrolase, Lipopolysaccharide Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Taylor, S. N. Sugiman-Marangos, K. Zhang, G. Deleon, G. D. Wright, M. S. Junop
Crystal Structure Of D, D-Heptose 1. 7-Bisphosphate Phosphatase From E. Coli.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - D,D-HEPTOSE 1,7-BISPHOSPHATE PHOSPHATASE
    Chains: A
    EC Number: 3.1.3.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST17
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: B0200, GMHB, JW0196, YAED
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: D-GLYCERO-D-MANNO-HEPTOSE 1,7-BISPHOSPHATE PHOSPHATASE

 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
1CA1Ligand/IonCALCIUM ION
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:112 , HIS A:114 , CYS A:127 , CYS A:129 , ARG A:130BINDING SITE FOR RESIDUE ZN A 212
2AC2SOFTWAREASP A:31 , ASP A:33 , ASP A:156 , HOH A:384 , HOH A:385 , HOH A:386BINDING SITE FOR RESIDUE CA A 213

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:131 -Pro A:132

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ESQ)

(-) 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:182
 aligned with GMHBB_ECOLI | P63228 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:182
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183  
          GMHBB_ECOLI     4 SVPAIFLDRDGTINVDHGYVHEIDNFEFIDGVIDAMRELKKMGFALVVVTNQSGIARGKFTEAQFETLTEWMDWSLADRDVDLDGIYYCPHHPQGSVEEFRQVCDCRKPHPGMLLSARDYLHIDMAASYMVGDKLEDMQAAVAANVGTKVLVRTGKPITPEAENAADWVLNSLADLPQAIKK 185
               SCOP domains d3esqa_ A: D,D-heptose 1,7-bisphosphate phosphatase GmhB                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..............hhhhh....hhhhhhhhhhhh..eeeeeeehhhhhhh..hhhhhhhhhhhhhhhhhh......eeeee.......hhhhh.........hhhhhhhhhhhh......eeee.hhhhhhhhhhhh..eeeee......hhhhhhhh.eee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3esq A  24 SVPAIFLDRDGTINVDHGYVHEIDNFEFIDGVIDAMRELKKMGFALVVVTNQSGIARGKFTEAQFETLTEWMDWSLADRDVDLDGIYYCPHHPQGSVEEFRQVCDCRKPHPGMLLSARDYLHIDMAASYMVGDKLEDMQAAVAANVGTKVLVRTGKPITPEAENAADWVLNSLADLPQAIKK 205
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203
   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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GMHBB_ECOLI | P63228)
molecular function
    GO:0034200    D,D-heptose 1,7-bisphosphate phosphatase activity    Catalysis of the reaction: D-beta-D-heptose 1,7-bisphosphate + H2O = D-beta-D-heptose 1-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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0097171    ADP-L-glycero-beta-D-manno-heptose biosynthetic process    The chemical reactions and pathways resulting in the formation of ADP-L-glycero-beta-D-manno-heptose, an ADP-L-glycero-D-manno-heptose having beta-configuration at the anomeric centre of the heptose. ADP-L-glycero-beta-D-manno-heptose (also called ADP-L-beta-D-heptose or ADP-L-glycero-D-manno-heptose) is a nucleotide-sugar precursor of the inner core lipopolysaccharide (LPS) from D-glycero-beta-D-manno-heptose 7-phosphate.
    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:0009103    lipopolysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
    GO:0009244    lipopolysaccharide core region biosynthetic process    The chemical reactions and pathways resulting in the formation of the core region of bacterial lipopolysaccharides, which contains ten saccharide residues.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GMHBB_ECOLI | P63228: 2gmw 3esr 3l1u 3l1v 3l8e 3l8f 3l8g

(-) Related Entries Specified in the PDB File

3esr