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(-) Description

Title :  CRYSTAL STRUCTURE OF D,D-HEPTOSE 1.7-BISPHOSPHATE PHOSPHATASE FROM E. COLI.
 
Authors :  K. Zhang, G. Deleon, G. D. Wright, M. S. Junop
Date :  07 Apr 06  (Deposition) - 10 Apr 07  (Release) - 16 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Zn-Binding Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. L. Taylor, S. Sugiman-Marangos, K. Zhang, M. A. Valvano, G. D. Wright, M. S. Junop
Structural And Kinetic Characterization Of The Lps Biosynthetic Enzyme D-Alpha, Beta-D-Heptose-1, 7-Bisphosphate Phosphatase (Gmhb) From Escherichia Coli.
Biochemistry V. 49 1033 2010
PubMed-ID: 20050699  |  Reference-DOI: 10.1021/BI901780J

(-) Compounds

Molecule 1 - D,D-HEPTOSE 1,7-BISPHOSPHATE PHOSPHATASE
    Chains: A, B
    EC Number: 3.1.3.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GMHB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: D-GLYCERO-D-MANNO-HEPTOSE 1,7-BISPHOSPHATE PHOSPHATASE

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/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 300
2AC2SOFTWARECYS B:112 , HIS B:114 , CYS B:127 , CYS B:129 , ARG B:130BINDING SITE FOR RESIDUE ZN B 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GMW)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:131 -Pro A:132
2Lys B:131 -Pro B:132

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GMW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GMW)

(-) Exons   (0, 0)

(no "Exon" information available for 2GMW)

(-) 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: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 d2gmwa1 A:24-205 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..hhhhhhhhhhhhhhhhhhh.....eeeee.......hhhhh.........hhhhhhhhhhhh.hhhh.eeee.hhhhhhhhhhh...eeeee......hhhhhhhh.eee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gmw A  24 SVPAIFLDRDGTINVDHGYVHEIDNFEFIDGVIDAMRELKKMGFALVVVTNQSGIARGKFTEAQFETLTEWMDWSLADRDVDLDGIYYCPHHPQGSVEEFRQVCDCRKPHPGMLLSARDYLHIDMAASYMVGDKLEDMQAAVAANVGTKVLVRTGKPITPEAENAADWVLNSLADLPQAIKK 205
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203  


Chain B from PDB  Type:PROTEIN  Length:184
 aligned with GMHBB_ECOLI | P63228 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:184
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183    
          GMHBB_ECOLI     4 SVPAIFLDRDGTINVDHGYVHEIDNFEFIDGVIDAMRELKKMGFALVVVTNQSGIARGKFTEAQFETLTEWMDWSLADRDVDLDGIYYCPHHPQGSVEEFRQVCDCRKPHPGMLLSARDYLHIDMAASYMVGDKLEDMQAAVAANVGTKVLVRTGKPITPEAENAADWVLNSLADLPQAIKKQQ 187
               SCOP domains d2gmwb_ B: 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.........hhhhhhhhhhhhhhhhhh......eeeee.......hhhhh.........hhhhhhhhhhhh.hhhh.eeee.hhhhhhhhhhh...eeeee......hhhhhhhh.eee.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gmw B  24 SVPAIFLDRDGTINVDHGYVHEIDNFEFIDGVIDAMRELKKMGFALVVVTNQSGIARGKFTEAQFETLTEWMDWSLADRDVDLDGIYYCPHHPQGSVEEFRQVCDCRKPHPGMLLSARDYLHIDMAASYMVGDKLEDMQAAVAANVGTKVLVRTGKPITPEAENAADWVLNSLADLPQAIKKQQ 207
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203
   Legend:   → Mismatch (orange background)
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  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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2GMW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GMW)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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

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        GMHBB_ECOLI | P63228: 3esq 3esr 3l1u 3l1v 3l8e 3l8f 3l8g

(-) Related Entries Specified in the PDB File

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