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(-) Description

Title :  CRYSTAL STRUCTURE OF GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE FROM THERMUS THERMOPHILUS HB8
 
Authors :  J. Ishijima, K. Ida, K. Yutani, M. Miyano, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  05 Jan 04  (Deposition) - 18 Jan 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (1x)
Keywords :  Glycerophosphoryl Diester Phosphodiesterase, Glycerophosphodiester Phosphodiesterase, Thermus Thermophilus, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Ishijima, K. Ida, K. Yutani, M. Miyano
Crystal Structure Of Glycerophosphoryl Diester Phosphodiesterase From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE
    Chains: A
    EC Number: 3.1.4.46
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A
Biological Unit 2 (1x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1V8E)

(-) Sites  (0, 0)

(no "Site" information available for 1V8E)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:161 -A:161

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Trp A:192 -Thr A:193

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V8E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V8E)

(-) Exons   (0, 0)

(no "Exon" information available for 1V8E)

(-) 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:217
 aligned with Q53W25_THET8 | Q53W25 from UniProtKB/TrEMBL  Length:224

    Alignment length:217
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       
         Q53W25_THET8     8 PLRLGHRGAPLKAKENTLESFRLALEAGLDGVELDVWPTRDGVFAVRHDPDTPLGPVFQVDYADLKAQEPDLPRLEEVLALKEAFPQAVFNVELKSFPGLGEEAARRLAALLRGREGVWVSSFDPLALLALRKAAPGLPLGFLMAEDHSALLPCLGVEAVHPHHALVTEEAVAGWRKRGLFVVAWTVNEEGEARRLLALGLDGLIGDRPEVLLPLGG 224
               SCOP domains d1v8ea1 A:8-224 Putative glycerophosphodiester phosphodiesterase TTHB141                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----GDPD-1v8eA01 A:13-218                                                                                                                                                                                         ------ Pfam domains
         Sec.struct. author .eeeee..........hhhhhhhhhhh...eeeeeeee.....eee....ee..ee.hhhhhhhhhhhh....hhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhh....eeeee...hhhhhhhh...eeee.hhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh...eeee.hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v8e A   8 PLRLGHRGAPLKAKENTLESFRLALEAGLDGVELDVWPTRDGVFAVRHDPDTPLGPVFQVDYADLKAQEPDLPRLEEVLALKEAFPQAVFNVELKSFPGLGEEAARRLAALLRGREGVWVSSFDPLALLALRKAAPGLPLGFLMAEDHSALLPCLGVEAVHPHHALVTEEAVAGWRKRGLFVVAWTVNEEGEARRLLALGLDGLIGDRPEVLLPLGG 224
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217
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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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1V8E)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: PLC (20)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q53W25_THET8 | Q53W25)
molecular function
    GO:0008889    glycerophosphodiester phosphodiesterase activity    Catalysis of the reaction: a glycerophosphodiester + H2O = an alcohol + sn-glycerol 3-phosphate.
    GO:0008081    phosphoric diester hydrolase activity    Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
biological process
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.

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    Trp A:192 - Thr A:193   [ RasMol ]  
 
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 Related Entries

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        Q53W25_THET8 | Q53W25: 1vd6

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