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(-) Description

Title :  CRYSTAL STRUCTURE OF PERIPLASMIC GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE FROM ESCHERICHIA COLI
 
Authors :  V. N. Malashkevich, E. Fedorov, S. C. Almo, S. K. Burley, New York Sgx Center For Structural Genomics (Nysgxrc)
Date :  27 Dec 04  (Deposition) - 25 Jan 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phosphodiesterase, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. M. Malashkevich, E. Fedorov, S. C. Almo
Crystal Structure Of Periplasmic Glycerophosphodiester Phosphodiesterase From Escherichia Coli
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE
    Chains: A, B
    EC Number: 3.1.4.46
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Gene: GLPQ
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE

 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 B:63 , ASP B:65 , GLU B:171 , GOL B:901 , HOH B:906 , HOH B:1052BINDING SITE FOR RESIDUE CA B 903
2AC2SOFTWAREGLU A:63 , ASP A:65 , GLU A:171 , GOL A:902 , HOH A:905 , HOH A:1043BINDING SITE FOR RESIDUE CA A 904
3AC3SOFTWAREHIS B:36 , GLU B:63 , GLU B:171 , GLN B:208 , PHE B:210 , LEU B:235 , TYR B:313 , CA B:903 , HOH B:906 , HOH B:1104BINDING SITE FOR RESIDUE GOL B 901
4AC4SOFTWAREHIS A:36 , GLU A:63 , GLU A:171 , GLN A:208 , PHE A:210 , LEU A:235 , TYR A:313 , CA A:904 , HOH A:905 , HOH A:1098 , HOH A:1185BINDING SITE FOR RESIDUE GOL A 902

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:313 -Thr A:314
2Tyr B:313 -Thr B:314

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GP_PDEPS51704 GP-PDE domain profile.GLPQ_ECOLI31-355
 		  2A:31-355
B:31-355

(-) Exons   (0, 0)

(no "Exon" information available for 1YDY)

(-) 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:328
 aligned with GLPQ_ECOLI | P09394 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:328
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348        
           GLPQ_ECOLI    29 NEKIVIAHRGASGYLPEHTLPAKAMAYAQGADYLEQDLVMTKDDNLVVLHDHYLDRVTDVADRFPDRARKDGRYYAIDFTLDEIKSLKFTEGFDIENGKKVQTYPGRFPMGKSDFRVHTFEEEIEFVQGLNHSTGKNIGIYPEIKAPWFHHQEGKDIAAKTLEVLKKYGYTGKDDKVYLQCFDADELKRIKNELEPKMGMELNLVQLIAYTDWNETQQKQPDGSWVNYNYDWMFKPGAMKQVAEYADGIGPDYHMLIEETSQPGNIKLTGMVQDAQQNKLVVHPYTVRSDKLPEYTPDVNQLYDALYNKAGVNGLFTDFPDKAVKFLN 356
               SCOP domains d1ydya_ A: Glycerophosphodiester phosphodiesterase GlpQ                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1ydyA00 A:29-356 Phosphatidylinositol (PI) phosphodiesterase                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...........hhhhhhhhhhh...eeeeeeee.....eee..........hhhhhh..........hhhhhhhhhhhhh.....eeee..eeee................hhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhh..hhhhhhhhhhhhh.........eeee.hhhhhhhhhhhhhhhhh...eeeeee.hhhhh..eee.....eee..hhhhhh.hhhhhhh....eeee.hhhh.............hhhhhhhhh..ee...............hhhhhhhhhhh.....eeee.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GP_PDE  PDB: A:31-355 UniProt: 31-355                                                                                                                                                                                                                                                                                                - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ydy A  29 NEKIVIAHRGASGYLPEHTLPAKAMAYAQGADYLEQDLVMTKDDNLVVLHDHYLDRVTDVADRFPDRARKDGRYYAIDFTLDEIKSLKFTEGFDIENGKKVQTYPGRFPMGKSDFRVHTFEEEIEFVQGLNHSTGKNIGIYPEIKAPWFHHQEGKDIAAKTLEVLKKYGYTGKDDKVYLQCFDADELKRIKNELEPKMGMELNLVQLIAYTDWNETQQKQPDGSWVNYNYDWMFKPGAMKQVAEYADGIGPDYHMLIEETSQPGNIKLTGMVQDAQQNKLVVHPYTVRSDKLPEYTPDVNQLYDALYNKAGVNGLFTDFPDKAVKFLN 356
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348        


Chain B from PDB  Type:PROTEIN  Length:328
 aligned with GLPQ_ECOLI | P09394 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:328
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348        
           GLPQ_ECOLI    29 NEKIVIAHRGASGYLPEHTLPAKAMAYAQGADYLEQDLVMTKDDNLVVLHDHYLDRVTDVADRFPDRARKDGRYYAIDFTLDEIKSLKFTEGFDIENGKKVQTYPGRFPMGKSDFRVHTFEEEIEFVQGLNHSTGKNIGIYPEIKAPWFHHQEGKDIAAKTLEVLKKYGYTGKDDKVYLQCFDADELKRIKNELEPKMGMELNLVQLIAYTDWNETQQKQPDGSWVNYNYDWMFKPGAMKQVAEYADGIGPDYHMLIEETSQPGNIKLTGMVQDAQQNKLVVHPYTVRSDKLPEYTPDVNQLYDALYNKAGVNGLFTDFPDKAVKFLN 356
               SCOP domains d1ydyb_ B: Glycerophosphodiester phosphodiesterase GlpQ                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1ydyB00 B:29-356 Phosphatidylinositol (PI) phosphodiesterase                                                                                                                                                                                                                                                                             CATH domains
           Pfam domains (1) -------GDPD-1ydyB01 B:36-350                                                                                                                                                                                                                                                                                                      ------ Pfam domains (1)
           Pfam domains (2) -------GDPD-1ydyB02 B:36-350                                                                                                                                                                                                                                                                                                      ------ Pfam domains (2)
         Sec.struct. author ...eeee...........hhhhhhhhhhh...eeeeeeee.....eee..........hhhhhh..........hhhhhhhhhhhh......eee....eee................hhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhh..hhhhhhhhhhhhh.........eeee.hhhhhhhhhhhhhhhhh...eeeeee.hhhhh..eee.....eee..hhhhhh.hhhhhhhh...eeee.hhhh.............hhhhhhhhh..ee...............hhhhhhhhhhh.....eeee.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GP_PDE  PDB: B:31-355 UniProt: 31-355                                                                                                                                                                                                                                                                                                - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ydy B  29 NEKIVIAHRGASGYLPEHTLPAKAMAYAQGADYLEQDLVMTKDDNLVVLHDHYLDRVTDVADRFPDRARKDGRYYAIDFTLDEIKSLKFTEGFDIENGKKVQTYPGRFPMGKSDFRVHTFEEEIEFVQGLNHSTGKNIGIYPEIKAPWFHHQEGKDIAAKTLEVLKKYGYTGKDDKVYLQCFDADELKRIKNELEPKMGMELNLVQLIAYTDWNETQQKQPDGSWVNYNYDWMFKPGAMKQVAEYADGIGPDYHMLIEETSQPGNIKLTGMVQDAQQNKLVVHPYTVRSDKLPEYTPDVNQLYDALYNKAGVNGLFTDFPDKAVKFLN 356
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348
   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  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GLPQ_ECOLI | P09394)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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: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:0006071    glycerol metabolic process    The chemical reactions and pathways involving glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
    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.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GLPQ_ECOLI | P09394: 1t8q

(-) Related Entries Specified in the PDB File

1t8q RELATED ID: NYSGXRC-T1974 RELATED DB: TARGETDB