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(-) Description

Title :  CRYSTAL STRUCTURE OF GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE COMPLEXED WITH GLYCEROL
 
Authors :  J. Ishijima, K. Yutani, Riken Structural Genomics/Proteomics Ini (Rsgi)
Date :  18 Mar 04  (Deposition) - 05 Apr 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Glycerophosphoryl Diester Phosphodiesterase, Glycerophosphodiester Phosphodiesterase, Thermus Thermophilus, Hb8, Glycerol Complex, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Ishijima, K. Yutani
Crystal Structure Of Glycerophosphoryl Diester Phosphodiesterase Complexed With Glycerol
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:13 , GLU A:40 , GLU A:100 , PHE A:130 , TRP A:192 , THR A:193 , HOH A:502 , HOH A:659 , HOH A:660BINDING SITE FOR RESIDUE GOL A 300

(-) 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 1VD6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VD6)

(-) Exons   (0, 0)

(no "Exon" information available for 1VD6)

(-) 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:218
 aligned with Q53W25_THET8 | Q53W25 from UniProtKB/TrEMBL  Length:224

    Alignment length:218
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216        
         Q53W25_THET8     7 RPLRLGHRGAPLKAKENTLESFRLALEAGLDGVELDVWPTRDGVFAVRHDPDTPLGPVFQVDYADLKAQEPDLPRLEEVLALKEAFPQAVFNVELKSFPGLGEEAARRLAALLRGREGVWVSSFDPLALLALRKAAPGLPLGFLMAEDHSALLPCLGVEAVHPHHALVTEEAVAGWRKRGLFVVAWTVNEEGEARRLLALGLDGLIGDRPEVLLPLGG 224
               SCOP domains d1vd6a_ A: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------GDPD-1vd6A01 A:13-218                                                                                                                                                                                         ------ Pfam domains
         Sec.struct. author ..eeeee..........hhhhhhhhhhh...eeeeeeee.....eee....ee..ee.hhhhhhhhhhhh....hhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhh....eeeee...hhhhhhhh...eeee.hhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhh...eeee.hhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vd6 A   7 RPLRLGHRGAPLKAKENTLESFRLALEAGLDGVELDVWPTRDGVFAVRHDPDTPLGPVFQVDYADLKAQEPDLPRLEEVLALKEAFPQAVFNVELKSFPGLGEEAARRLAALLRGREGVWVSSFDPLALLALRKAAPGLPLGFLMAEDHSALLPCLGVEAVHPHHALVTEEAVAGWRKRGLFVVAWTVNEEGEARRLLALGLDGLIGDRPEVLLPLGG 224
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216
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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 1VD6)

(-) 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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        Q53W25_THET8 | Q53W25: 1v8e

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