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(-) Description

Title :  CRYSTAL STRUCTURE OF A GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE (BDI_0402) FROM PARABACTEROIDES DISTASONIS ATCC 8503 AT 1.89 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  24 Jun 10  (Deposition) - 28 Jul 10  (Release) - 28 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Glycerophosphodiester Phosphodiesterase (Bdi_0402) From Parabacteroides Distasoni Atcc 8503 At 1. 89 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BDI_0402
    Organism Scientific: PARABACTEROIDES DISTASONIS
    Organism Taxid: 435591
    Strain: ATCC 8503 / DSM 20701 / NCTC 11152

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MG2Ligand/IonMAGNESIUM ION
3MSE8Mod. Amino AcidSELENOMETHIONINE
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:59 , ASP A:61 , GLU A:123 , GOL A:303 , HOH A:305 , HOH A:310BINDING SITE FOR RESIDUE MG A 301
2AC2SOFTWAREGLY A:0 , HOH A:454BINDING SITE FOR RESIDUE MG A 302
3AC3SOFTWAREHIS A:30 , GLU A:59 , GLU A:123 , ILE A:156 , LEU A:178 , MG A:301 , HOH A:305 , HOH A:310 , HOH A:326 , HOH A:576BINDING SITE FOR RESIDUE GOL A 303
4AC4SOFTWARELYS A:145 , LYS A:148 , LEU A:149 , ALA A:150 , LYS A:151 , HOH A:443 , HOH A:594BINDING SITE FOR RESIDUE PEG A 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NO3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp A:222 -Thr A:223

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NO3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NO3)

(-) Exons   (0, 0)

(no "Exon" information available for 3NO3)

(-) 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:238
 aligned with A6L916_PARD8 | A6L916 from UniProtKB/TrEMBL  Length:258

    Alignment length:238
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250        
         A6L916_PARD8    21 AKDNTKVIAHRGYWKTEGSAQNSIRSLERASEIGAYGSEFDVHLTADNVLVVYHDNDIQGKHIQSCTYDELKDLQLSNGEKLPTLEQYLKRAKKLKNIRLIFELKSHDTPERNRDAARLSVQMVKRMKLAKRTDYISFNMDACKEFIRLCPKSEVSYLNGELSPMELKELGFTGLDYHYKVLQSHPDWVKDCKVLGMTSNVWTVDDPKLMEEMIDMGVDFITTDLPEETQKILHSRAQ 258
               SCOP domains d3no3a_ A: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------GDPD-3no3A01 A:30-248                                                                                                                                                                                                      ---------- Pfam domains
         Sec.struct. author .....eeee.............hhhhhhhhhhh...eeeeeeee.....eee....ee..ee.hhhhhhhhh...........hhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh....eee.....hhhhhhhh...eeeeehhhhhhh.hhhhhhhhh..eeeee...hhhhhhhhhhhh..eeee.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3no3 A   0 GKDNTKVIAHRGYWKTEGSAQNSIRSLERASEIGAYGSEFDVHLTADNVLVVYHDNDIQGKHIQSCTYDELKDLQLSNGEKLPTLEQYLKRAKKLKNIRLIFELKSHDTPERNRDAARLSVQmVKRmKLAKRTDYISFNmDACKEFIRLCPKSEVSYLNGELSPmELKELGFTGLDYHYKVLQSHPDWVKDCKVLGmTSNVWTVDDPKLmEEmIDmGVDFITTDLPEETQKILHSRAQ 258
                            ||      30        40        50        60        70        80        90       100       110       120       130       140  |   |150       160       170       180    |  190       200       210      |220       230  |  | 240       250        
                            ||                                                                                                                      143-MSE          160-MSE                  185-MSE                         217-MSE      230-MSE |                      
                            0|                                                                                                                          147-MSE                                                                               233-MSE                     
                            22                                                                                                                                                                                                                   236-MSE
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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  (0, 0)

(no "CATH Domain" information available for 3NO3)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A6L916_PARD8 | A6L916)
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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