Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF D,D-HEPTOSE1.7-BISPHOSPHATE PHOSPHATASE FROM E. COLI IN COMPLEX WITH CALCIUM AND PHOSPHATE
 
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 :  1.95
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  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2PO41Ligand/IonPHOSPHATE ION
3ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:112 , HIS A:114 , CYS A:127 , CYS A:129BINDING SITE FOR RESIDUE ZN A 212
2AC2SOFTWAREASP A:31 , ASP A:33 , ASP A:156 , PO4 A:214 , HOH A:304BINDING SITE FOR RESIDUE CA A 213
3AC3SOFTWAREASP A:31 , ARG A:32 , ASP A:33 , THR A:73 , ASN A:74 , LYS A:131 , CA A:213 , HOH A:243 , HOH A:316BINDING SITE FOR RESIDUE PO4 A 214

(-) SS Bonds  (0, 0)

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

(-) 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 3ESR)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ESR)

(-) 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 d3esra_ 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..eeeeeee.hhhhhh..hhhhhhhhhhhhhhhhhh......eeeee.....................hhhhhhhhhhhh......eeee.hhhhhhhhhhh...eeeee......hhhhhhhh.eee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3esr 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)
    → 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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:131 - Pro A:132   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3esr
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  GMHBB_ECOLI | P63228
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.3.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  GMHBB_ECOLI | P63228
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) Related Entries Specified in the PDB File

3esq