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(-) Description

Title :  CRYSTAL STRUCTURE OF GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE (GDPD) (TM1621) FROM THERMOTOGA MARITIMA AT 1.60 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  12 Feb 03  (Deposition) - 01 Apr 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Tm1621, Glycerophosphodiester Phosphodiesterase (Gdpd), Structural Genomics, Jcsg, Psi, Protein Structure Initiative, Joint Center For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Santelli, R. Schwarzenbacher, D. Mcmullan, T. Biorac, L. S. Brinen J. M. Canaves, J. Cambell, X. Dai, A. M. Deacon, M. A. Elsliger, S. Eshagi, R. Floyd, A. Godzik, C. Grittini, S. K. Grzechnik, L. Jaroszewski, C. Karlak, H. E. Klock, E. Koesema, J. S. Kovarik, A. Kreusch, P. Kuhn, S. A. Lesley, T. M. Mcphillips, M. D. Miller, A. Morse, K. Moy, J. Ouyang, R. Page, K. Quijano, F. Rezezadeh, A. Robb, R. C. Stevens, H. Van Den Bedem, J. Velasquez, J. Vincent, F. Von Delft, X. Wang, B. West, G. Wolf, Q. Xu, K. O. Hodgson, J. Wooley, I. A. Wilson
Crystal Structure Of A Glycerophosphodiester Phosphodiesterase (Gdpd) From Thermotoga Maritima (Tm1621) At 1. 60 A Resolution.
Proteins V. 56 167 2004
PubMed-ID: 15162496  |  Reference-DOI: 10.1002/PROT.20120

(-) Compounds

Molecule 1 - GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE
    Chains: A
    EC Number: 3.1.4.46
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM1621
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: GDPD

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:111 , LYS A:112 , ARG A:114 , ASP A:125 , HOH A:655 , HOH A:656BINDING SITE FOR RESIDUE NA A 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O1Z)

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O1Z)

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 1O1Z)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:226
 aligned with Q9X1V6_THEMA | Q9X1V6 from UniProtKB/TrEMBL  Length:222

    Alignment length:226
                                1                                                                                                                                                                                                                             
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216      
         Q9X1V6_THEMA     - ----MIVLGHRGYSAKYLENTLEAFMKAIEAGANGVELDVRLSKDGKVVVSHDEDLKRLFGLDVKIRDATVSELKELTDGKITTLKEVFENVSDDKIINIEIKEREAADAVLEISKKRKNLIFSSFDLDLLDEKFKGTKYGYLIDEENYGSIENFVERVEKERPYSLHVPYQAFELEYAVEVLRSFRKKGIVIFVWTLNDPEIYRKIRREIDGVITDEVELFVKLR 222
               SCOP domains d1o1za_ A: Hypothetical protein TM1621                                                                                                                                                                                             SCOP domains
               CATH domains 1o1zA00 A:-3-222 Phosphatidylinositol (PI) phosphodiesterase                                                                                                                                                                       CATH domains
               Pfam domains ---------GDPD-1o1zA01 A:6-217                                                                                                                                                                                                ----- Pfam domains
         Sec.struct. author .....eeeee..........hhhhhhhhhhh...eeeeeeee.....eee....eehhhhheeee.hhhhhhhhhhhh.....hhhhhhhhh....eeeeee.hhhhhhhhhhhhh....eeeee.hhhhhhhhh....eeee.......hhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh.eeee.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o1z A  -3 HHHHVIVLGHRGYSAKYLENTLEAFMKAIEAGANGVELDVRLSKDGKVVVSHDEDLKRLFGLDVKIRDATVSELKELTDGKITTLKEVFENVSDDKIINIEIKEREAADAVLEISKKRKNLIFSSFDLDLLDEKFKGTKYGYLIDEENYGSIENFVERVEKERPYSLHVPYQAFELEYAVEVLRSFRKKGIVIFVWTLNDPEIYRKIRREIDGVITDEVELFVKLR 222
                                     6        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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PLC (20)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9X1V6_THEMA | Q9X1V6)
molecular function
    GO:0008889    glycerophosphodiester phosphodiesterase activity    Catalysis of the reaction: a glycerophosphodiester + H2O = an alcohol + sn-glycerol 3-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: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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