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(-) Description

Title :  CRYSTAL STRUCTURE OF GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE (GDPD) FROM T. TENGCONGENSIS
 
Authors :  L. Shi, J. F. Liu, X. M. An, D. C. Liang
Date :  17 May 07  (Deposition) - 01 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glycerophosphodiester Phosphodiesterase, T. Tengcongensis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Shi, J. F. Liu, X. M. An, D. C. Liang
Crystal Structure Of Glycerophosphodiester Phosphodiesteras (Gdpd) From Thermoanaerobacter Tengcongensis, A Metal Ion-Dependent Enzyme: Insight Into The Catalytic Mechanism.
Proteins V. 72 280 2008
PubMed-ID: 18214974  |  Reference-DOI: 10.1002/PROT.21921

(-) Compounds

Molecule 1 - GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHAT2
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOANAEROBACTER TENGCONGENSIS
    Organism Taxid: 273068
    Strain: MB4

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GOL2Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:44 , ASP A:46 , GLU A:119 , HOH A:503 , HOH A:628BINDING SITE FOR RESIDUE CA A 501
2AC2SOFTWAREGLU B:44 , ASP B:46 , GLU B:119 , HOH B:503 , HOH B:607BINDING SITE FOR RESIDUE CA B 502
3AC3SOFTWAREHIS B:17 , GLU B:44 , GLU B:119 , PHE B:152 , LEU B:172 , HOH B:504 , HOH B:538 , HOH B:607BINDING SITE FOR RESIDUE GOL B 400
4AC4SOFTWAREHIS A:17 , GLU A:44 , GLU A:119 , PHE A:152 , LEU A:172 , TRP A:217 , HOH A:503 , HOH A:505 , HOH A:521 , HOH A:527BINDING SITE FOR RESIDUE GOL A 401

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:175 -B:175

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PZ0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PZ0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PZ0)

(-) Exons   (0, 0)

(no "Exon" information available for 2PZ0)

(-) 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:239
 aligned with Q8RB32_CALS4 | Q8RB32 from UniProtKB/TrEMBL  Length:243

    Alignment length:239
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231         
         Q8RB32_CALS4     2 KTLVIAHRGDSKNVPENTIAAFKRAMELGADGIELDVQLTKDGHLVVIHDETVDRTTNGEGFVKDFTLEEIKKLDAGIKFGEKFAGERIPTLYEVFELIGDKDFLVNIEIKSGIVLYPGIEEKLIKAIKEYNFEERVIISSFNHYSLRDVKKMAPHLKIGLLYQCGLVEPWHMALRMEAYSLHPFYFNIIPELVEGCKKNGVKLFPWTVDRKEDMERMIKAGVDGIITDDPETLINLVR 240
               SCOP domains d2pz0a_ A: automated matches                                                                                                                                                                                                                    SCOP domains
               CATH domains 2pz0A00 A:11-249 Phosphatidylinositol (PI) phosphodiesterase                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..........hhhhhhhhhhhh..eeeeeeee.....eee..............hhhhhhhhhhh........hhhhh.....hhhhhhhhhh....eeeeee........hhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhh...eeeeee......hhhhhhhh...eeee.hhhhhhhhhhhhhhh..ee......hhhhhhhhhhhh..eeee.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pz0 A  11 KTLVIAHRGDSKNVPENTIAAFKRAMELGADGIELDVQLTKDGHLVVIHDETVDRTTNGEGFVKDFTLEEIKKLDAGIKFGEKFAGERIPTLYEVFELIGDKDFLVNIEIKSGIVLYPGIEEKLIKAIKEYNFEERVIISSFNHYSLRDVKKMAPHLKIGLLYQCGLVEPWHMALRMEAYSLHPFYFNIIPELVEGCKKNGVKLFPWTVDRKEDMERMIKAGVDGIITDDPETLINLVR 249
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         


Chain B from PDB  Type:PROTEIN  Length:243
 aligned with Q8RB32_CALS4 | Q8RB32 from UniProtKB/TrEMBL  Length:243

    Alignment length:243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
         Q8RB32_CALS4     1 MKTLVIAHRGDSKNVPENTIAAFKRAMELGADGIELDVQLTKDGHLVVIHDETVDRTTNGEGFVKDFTLEEIKKLDAGIKFGEKFAGERIPTLYEVFELIGDKDFLVNIEIKSGIVLYPGIEEKLIKAIKEYNFEERVIISSFNHYSLRDVKKMAPHLKIGLLYQCGLVEPWHMALRMEAYSLHPFYFNIIPELVEGCKKNGVKLFPWTVDRKEDMERMIKAGVDGIITDDPETLINLVRKGG 243
               SCOP domains d2pz0b_ B: automated matches                                                                                                                                                                                                                        SCOP domains
               CATH domains 2pz0B00 B:10-252 Phosphatidylinositol (PI) phosphodiesterase                                                                                                                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..........hhhhhhhhhhhh..eeeeeeee.....eee..............hhhhhhhhhhh........hhhhh.....hhhhhhhhhh....eeeeee........hhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhh...eeeeee......hhhhhhhh...eeee.hhhhhhhhhhhhhh...ee......hhhhhhhhhhhh..eeee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pz0 B  10 MKTLVIAHRGDSKNVPENTIAAFKRAMELGADGIELDVQLTKDGHLVVIHDETVDRTTNGEGFVKDFTLEEIKKLDAGIKFGEKFAGERIPTLYEVFELIGDKDFLVNIEIKSGIVLYPGIEEKLIKAIKEYNFEERVIISSFNHYSLRDVKKMAPHLKIGLLYQCGLVEPWHMALRMEAYSLHPFYFNIIPELVEGCKKNGVKLFPWTVDRKEDMERMIKAGVDGIITDDPETLINLVRKGG 252
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249
   Legend:   → Mismatch (orange background)
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  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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2PZ0)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8RB32_CALS4 | Q8RB32)
molecular function
    GO:0008889    glycerophosphodiester phosphodiesterase activity    Catalysis of the reaction: a glycerophosphodiester + H2O = an alcohol + sn-glycerol 3-phosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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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