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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE (YP_165505.1) FROM SILICIBACTER POMEROYI DSS-3 AT 1.60 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  10 Dec 09  (Deposition) - 29 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Putative Glycerophosphoryl Diester Phosphodiesterase, 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 Putative Glycerophosphoryl Diester Phosphodiesterase (Yp_165505. 1) From Silicibacter Pomeroyi Dss-3 At 1. 60 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SPO0236
    Organism Scientific: SILICIBACTER POMEROYI
    Organism Taxid: 89184

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 31)

Asymmetric/Biological Unit (4, 31)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2MG3Ligand/IonMAGNESIUM ION
3MSE21Mod. Amino AcidSELENOMETHIONINE
4UNL2Ligand/IonUNKNOWN LIGAND

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:49 , ASP A:51 , GLU A:148 , HOH A:327 , HOH A:353BINDING SITE FOR RESIDUE MG A 313
2AC2SOFTWARETHR A:108 , VAL A:109 , HOH A:659 , ARG B:127BINDING SITE FOR RESIDUE CL A 314
3AC3SOFTWAREARG A:26 , ARG A:113 , HOH A:401BINDING SITE FOR RESIDUE CL A 315
4AC4SOFTWAREARG A:18 , THR A:312 , HOH A:404 , HOH A:476BINDING SITE FOR RESIDUE CL A 316
5AC5SOFTWAREGLU B:49 , ASP B:51 , GLU B:148 , HOH B:323 , HOH B:364BINDING SITE FOR RESIDUE MG B 313
6AC6SOFTWAREHOH A:345 , HOH A:532 , HOH A:598 , HOH A:603 , HOH A:621 , HIS B:79BINDING SITE FOR RESIDUE MG B 314
7AC7SOFTWAREARG B:174 , HOH B:396 , HOH B:462BINDING SITE FOR RESIDUE CL B 315
8AC8SOFTWAREARG B:26 , ARG B:113BINDING SITE FOR RESIDUE CL B 316

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L12)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:273 -Thr A:274
2Trp B:273 -Thr B:274

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L12)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L12)

(-) Exons   (0, 0)

(no "Exon" information available for 3L12)

(-) 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:297
 aligned with Q5LX22_RUEPO | Q5LX22 from UniProtKB/TrEMBL  Length:312

    Alignment length:310
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312
         Q5LX22_RUEPO     3 GFSQLEGLRGHPSVVRVIGHRGARGVMPENTLEGFAFTLAAGVRALEFDVVMTADGVPVVTHNHHLANAMTRDGQGHWLTGAERQVAEMTYAEIRALDVGGLDGRTVYGRRFPDQAFLTGIHVPRLGELLDLCAGYGDQAPYLLLELKSDPALMHDHAARAEMVAAVLADVRRYRMEPRTVMHSFDWALLGECRRQAPDLPTSYLSQLPENADDPGEDSAKPVGPDYDRMTESLPQAVASAGGQLWCPYFLDVTPELVAEAHDLGLIVLTWTVNEPEDIRRMATTGVDGIVTDYPGRTQRILIDMGLSWT 312
               SCOP domains d3l12a_ A: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh.......eeeee..........hhhhhhhhhhh...eeeeeeee.....eee........................hhhhhhhhhhhh.........hhhhhhh............hhhhhhhhhhhhhhhh.eeeeee..hhhhh.hhhhhhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh....eeeee....-------------.........hhhhhhhhhh..eeee.hhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh...eeee.hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l12 A   3 GFSQLEGLRGHPSVVRVIGHRGARGVmPENTLEGFAFTLAAGVRALEFDVVmTADGVPVVTHNHHLANAmTRDGQGHWLTGAERQVAEmTYAEIRALDVGGLDGRTVYGRRFPDQAFLTGIHVPRLGELLDLCAGYGDQAPYLLLELKSDPALmHDHAARAEmVAAVLADVRRYRmEPRTVmHSFDWALLGECRRQAPDLPTSYLSQLPE-------------GPDYDRmTESLPQAVASAGGQLWCPYFLDVTPELVAEAHDLGLIVLTWTVNEPEDIRRmATTGVDGIVTDYPGRTQRILIDmGLSWT 312
                                    12        22      | 32        42        52 |      62        72        82        92       102       112       122       132       142       152   |   162  |    172     | 182 |     192       202       212         -   |   232       242       252       262       272       282 |     292       302    |  312
                                                     29-MSE                   54-MSE            72-MSE             91-MSE                                                          156-MSE  165-MSE      178-MSE |                         212           226     |                                                 284-MSE                307-MSE 
                                                                                                                                                                                                               184-MSE                                         232-MSE                                                                            


Chain B from PDB  Type:PROTEIN  Length:295
 aligned with Q5LX22_RUEPO | Q5LX22 from UniProtKB/TrEMBL  Length:312

    Alignment length:310
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312
         Q5LX22_RUEPO     3 GFSQLEGLRGHPSVVRVIGHRGARGVMPENTLEGFAFTLAAGVRALEFDVVMTADGVPVVTHNHHLANAMTRDGQGHWLTGAERQVAEMTYAEIRALDVGGLDGRTVYGRRFPDQAFLTGIHVPRLGELLDLCAGYGDQAPYLLLELKSDPALMHDHAARAEMVAAVLADVRRYRMEPRTVMHSFDWALLGECRRQAPDLPTSYLSQLPENADDPGEDSAKPVGPDYDRMTESLPQAVASAGGQLWCPYFLDVTPELVAEAHDLGLIVLTWTVNEPEDIRRMATTGVDGIVTDYPGRTQRILIDMGLSWT 312
               SCOP domains d3l12b_ B: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh.......eeeee..........hhhhhhhhhhh...eeeeeeee.....eee........................hhhhhhhhhhhh.........hhhhhhh............hhhhhhhhhhhhhhhh.eeeeee.....--.hhhhhhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh....eeeee....-------------.........hhhhhhhhhh..eeee.hhhhhhhhhhhhhhh..eeee....hhhhhhhhhh....eeee.hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l12 B   3 GFSQLEGLRGHPSVVRVIGHRGARGVmPENTLEGFAFTLAAGVRALEFDVVmTADGVPVVTHNHHLANAmTRDGQGHWLTGAERQVAEmTYAEIRALDVGGLDGRTVYGRRFPDQAFLTGIHVPRLGELLDLCAGYGDQAPYLLLELKSDPA--HDHAARAEmVAAVLADVRRYRmEPRTVmHSFDWALLGECRRQAPDLPTSYLSQLPE-------------GPDYDRmTESLPQAVASAGGQLWCPYFLDVTPELVAEAHDLGLIVLTWTVNEPEDIRRmATTGVDGIVTDYPGRTQRILIDmGLSWT 312
                                    12        22      | 32        42        52 |      62        72        82        92       102       112       122       132       142       152 |  |  162  |    172     | 182 |     192       202       212         -   |   232       242       252       262       272       282 |     292       302    |  312
                                                     29-MSE                   54-MSE            72-MSE             91-MSE                                                        154  |     165-MSE      178-MSE |                         212           226     |                                                 284-MSE                307-MSE 
                                                                                                                                                                                    157                        184-MSE                                         232-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (0, 0)

(no "CATH Domain" information available for 3L12)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3L12)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5LX22_RUEPO | Q5LX22)
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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