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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE FROM SHIGELLA FLEXNERI 2A
 
Authors :  R. Zhang, R. Wu, S. Clancy, S. Jiang, A. Joachimiak, Midwest Center Fo Structural Genomics (Mcsg)
Date :  07 Feb 07  (Deposition) - 06 Mar 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Glycerophosphodiester Phosphodiesterase, Structural Genomics, Mcsg, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Zhang, R. Wu, S. Clancy, S. Jiang, A. Joachimiak
The Crystal Structure Of The Glycerophosphodiester Phosphodiesterase From Shigella Flexneri 2A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE
    Atcc: 700930
    Chains: A, B, C, D
    EC Number: 3.1.4.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PDM68
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: UGPQ, SF3466, S_4296
    Organism Scientific: SHIGELLA FLEXNERI
    Organism Taxid: 623
    Strain: 2457T, 301

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 28)

Asymmetric Unit (2, 28)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE
2PO44Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 3 (2, 7)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 4 (2, 7)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:12 , ARG A:13 , GLU A:39 , ASP A:41 , GLU A:114 , PHE A:148 , TYR A:213BINDING SITE FOR RESIDUE PO4 A 301
2AC2SOFTWAREHIS B:12 , GLU B:39 , GLU B:114 , PHE B:148 , TYR B:213BINDING SITE FOR RESIDUE PO4 B 301
3AC3SOFTWAREHOH C:339 , HIS D:12 , GLU D:39 , GLU D:114 , PHE D:148 , TYR D:213BINDING SITE FOR RESIDUE PO4 C 301
4AC4SOFTWAREHIS C:12 , GLU C:39 , ASP C:41 , GLU C:114 , PHE C:148BINDING SITE FOR RESIDUE PO4 D 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OTD)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:213 -Thr A:214
2Tyr B:213 -Thr B:214
3Tyr C:213 -Thr C:214
4Tyr D:213 -Thr D:214

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2OTD)

(-) 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:245
 aligned with Q83PU8_SHIFL | Q83PU8 from UniProtKB/TrEMBL  Length:247

    Alignment length:245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241     
         Q83PU8_SHIFL     2 SNWPYPRIVAHRGGGKLAPENTLAAIDVGAKYGHKMIEFDAKLSKDGEIFLLHDDNLERTSNGWGVAGELNWQDLLRVDAGSWYSKAFKGEPLPLLSQVAERCREHGMMANIEIKPTTGTGPLTGKMVALAARQLWAGMTPPLLSSFEIDALEAAQQAAPELPRGLLLDEWRDDWRELTARLGCVSIHLNHKLLDKARVMQLKDAGLRILVYTVNKPQHAAELLRWGVDCICTDAIDVIGPNFTA 246
               SCOP domains d2otda_ A: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains ------2otdA01 A:8-235 Phosphatidylinositol (PI) phosphodiesterase                                                                                                                                                                         ----------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee...........hhhhhhhhhhh...eeeeeeee.....eee..............hhhhhhhhhhh........hhhhh.....hhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhh....eeeee.....hhhhhhhhhh..eeeee.hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh..eeee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2otd A   2 SNWPYPRIVAHRGGGKLAPENTLAAIDVGAKYGHKmIEFDAKLSKDGEIFLLHDDNLERTSNGWGVAGELNWQDLLRVDAGSWYSKAFKGEPLPLLSQVAERCREHGmmANIEIKPTTGTGPLTGKmVALAARQLWAGmTPPLLSSFEIDALEAAQQAAPELPRGLLLDEWRDDWRELTARLGCVSIHLNHKLLDKARVmQLKDAGLRILVYTVNKPQHAAELLRWGVDCICTDAIDVIGPNFTA 246
                                    11        21        31     |  41        51        61        71        81        91       101       111       121      |131       141       151       161       171       181       191       201       211       221       231       241     
                                                              37-MSE                                                                 109-MSE            128-MSE     140-MSE                                                      201-MSE                                         
                                                                                                                                      110-MSE                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:245
 aligned with Q83PU8_SHIFL | Q83PU8 from UniProtKB/TrEMBL  Length:247

    Alignment length:245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241     
         Q83PU8_SHIFL     2 SNWPYPRIVAHRGGGKLAPENTLAAIDVGAKYGHKMIEFDAKLSKDGEIFLLHDDNLERTSNGWGVAGELNWQDLLRVDAGSWYSKAFKGEPLPLLSQVAERCREHGMMANIEIKPTTGTGPLTGKMVALAARQLWAGMTPPLLSSFEIDALEAAQQAAPELPRGLLLDEWRDDWRELTARLGCVSIHLNHKLLDKARVMQLKDAGLRILVYTVNKPQHAAELLRWGVDCICTDAIDVIGPNFTA 246
               SCOP domains d2otdb_ B: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains ------2otdB01 B:8-235 Phosphatidylinositol (PI) phosphodiesterase                                                                                                                                                                         ----------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee..........hhhhhhhhhhh...eeeeeeee.....eee..............hhhhhhhhhhh........hhhhh.....hhhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhh.....eeee.....hhhhhhhhh...eeee.....hhhhhhhhhhhh.eee.....hhhhhhhhhhh....eee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2otd B   2 SNWPYPRIVAHRGGGKLAPENTLAAIDVGAKYGHKmIEFDAKLSKDGEIFLLHDDNLERTSNGWGVAGELNWQDLLRVDAGSWYSKAFKGEPLPLLSQVAERCREHGmmANIEIKPTTGTGPLTGKmVALAARQLWAGmTPPLLSSFEIDALEAAQQAAPELPRGLLLDEWRDDWRELTARLGCVSIHLNHKLLDKARVmQLKDAGLRILVYTVNKPQHAAELLRWGVDCICTDAIDVIGPNFTA 246
                                    11        21        31     |  41        51        61        71        81        91       101       111       121      |131       141       151       161       171       181       191       201       211       221       231       241     
                                                              37-MSE                                                                 109-MSE            128-MSE     140-MSE                                                      201-MSE                                         
                                                                                                                                      110-MSE                                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:245
 aligned with Q83PU8_SHIFL | Q83PU8 from UniProtKB/TrEMBL  Length:247

    Alignment length:245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241     
         Q83PU8_SHIFL     2 SNWPYPRIVAHRGGGKLAPENTLAAIDVGAKYGHKMIEFDAKLSKDGEIFLLHDDNLERTSNGWGVAGELNWQDLLRVDAGSWYSKAFKGEPLPLLSQVAERCREHGMMANIEIKPTTGTGPLTGKMVALAARQLWAGMTPPLLSSFEIDALEAAQQAAPELPRGLLLDEWRDDWRELTARLGCVSIHLNHKLLDKARVMQLKDAGLRILVYTVNKPQHAAELLRWGVDCICTDAIDVIGPNFTA 246
               SCOP domains d2otdc_ C: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains ------2otdC01 C:8-235 Phosphatidylinositol (PI) phosphodiesterase                                                                                                                                                                         ----------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee...........hhhhhhhhhhh...eeeeeeee.....eee.....hhhhh....hhhhhhhhhhh..................hhhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhh....eeeee.....hhhhhhhhhh..eeeee.hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh..eeee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2otd C   2 SNWPYPRIVAHRGGGKLAPENTLAAIDVGAKYGHKmIEFDAKLSKDGEIFLLHDDNLERTSNGWGVAGELNWQDLLRVDAGSWYSKAFKGEPLPLLSQVAERCREHGmmANIEIKPTTGTGPLTGKmVALAARQLWAGmTPPLLSSFEIDALEAAQQAAPELPRGLLLDEWRDDWRELTARLGCVSIHLNHKLLDKARVmQLKDAGLRILVYTVNKPQHAAELLRWGVDCICTDAIDVIGPNFTA 246
                                    11        21        31     |  41        51        61        71        81        91       101       111       121      |131       141       151       161       171       181       191       201       211       221       231       241     
                                                              37-MSE                                                                 109-MSE            128-MSE     140-MSE                                                      201-MSE                                         
                                                                                                                                      110-MSE                                                                                                                                    


Chain D from PDB  Type:PROTEIN  Length:245
 aligned with Q83PU8_SHIFL | Q83PU8 from UniProtKB/TrEMBL  Length:247

    Alignment length:245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241     
         Q83PU8_SHIFL     2 SNWPYPRIVAHRGGGKLAPENTLAAIDVGAKYGHKMIEFDAKLSKDGEIFLLHDDNLERTSNGWGVAGELNWQDLLRVDAGSWYSKAFKGEPLPLLSQVAERCREHGMMANIEIKPTTGTGPLTGKMVALAARQLWAGMTPPLLSSFEIDALEAAQQAAPELPRGLLLDEWRDDWRELTARLGCVSIHLNHKLLDKARVMQLKDAGLRILVYTVNKPQHAAELLRWGVDCICTDAIDVIGPNFTA 246
               SCOP domains d2otdd_ D: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains ------2otdD01 D:8-235 Phosphatidylinositol (PI) phosphodiesterase                                                                                                                                                                         ----------- CATH domains
           Pfam domains (1) ----------GDPD-2otdD01 D:12-239                                                                                                                                                                                                               ------- Pfam domains (1)
           Pfam domains (2) ----------GDPD-2otdD02 D:12-239                                                                                                                                                                                                               ------- Pfam domains (2)
           Pfam domains (3) ----------GDPD-2otdD03 D:12-239                                                                                                                                                                                                               ------- Pfam domains (3)
           Pfam domains (4) ----------GDPD-2otdD04 D:12-239                                                                                                                                                                                                               ------- Pfam domains (4)
         Sec.struct. author .......eee...........hhhhhhhhhhh...eeeeeeee.....eee.....hhhhh....hhhhhhhhhhh........hhhhh.....hhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhh....eeeee.....hhhhhhhhhh..eeeee.hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh..eeee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2otd D   2 SNWPYPRIVAHRGGGKLAPENTLAAIDVGAKYGHKmIEFDAKLSKDGEIFLLHDDNLERTSNGWGVAGELNWQDLLRVDAGSWYSKAFKGEPLPLLSQVAERCREHGmmANIEIKPTTGTGPLTGKmVALAARQLWAGmTPPLLSSFEIDALEAAQQAAPELPRGLLLDEWRDDWRELTARLGCVSIHLNHKLLDKARVmQLKDAGLRILVYTVNKPQHAAELLRWGVDCICTDAIDVIGPNFTA 246
                                    11        21        31     |  41        51        61        71        81        91       101       111       121      |131       141       151       161       171       181       191       201       211       221       231       241     
                                                              37-MSE                                                                 109-MSE            128-MSE     140-MSE                                                      201-MSE                                         
                                                                                                                                      110-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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: PLC (20)
(-)
Family: GDPD (8)
(-)
Shigella flexneri (1)
1aGDPD-2otdD01D:12-239
1bGDPD-2otdD02D:12-239
1cGDPD-2otdD03D:12-239
1dGDPD-2otdD04D:12-239

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q83PU8_SHIFL | Q83PU8)
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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