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(-) Description

Title :  CRYSTAL STRUCTURE OF GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE FROM AGROBACTERIUM TUMEFACIENS STR.C58
 
Authors :  N. R. Krishnamurthy, D. Kumaran, S. Swaminathan, S. K. Burley, New Yor Research Center For Structural Genomics (Nysgxrc)
Date :  11 Apr 05  (Deposition) - 03 May 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Nysgxrc, T2047, Glycerophosphodiester Phosphodiesterase, Agrobacterium Tumefaciens Str. C58, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. N. Rao, J. B. Bonanno, S. K. Burley, S. Swaminathan
Crystal Structure Of Glycerophosphodiester Phosphodiesteras From Agrobacterium Tumefaciens By Sad With A Large Asymmetric Unit.
Proteins V. 65 514 2006
PubMed-ID: 16909422  |  Reference-DOI: 10.1002/PROT.21079

(-) Compounds

Molecule 1 - GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: AGROBACTERIUM TUMEFACIENS STR.
    Organism Taxid: 176299
    Strain: C58

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2SO46Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:106 , GLU A:108 , MET A:153 , GLU A:175 , SO4 A:4770BINDING SITE FOR RESIDUE ACT A 801
02AC2SOFTWAREHIS A:7 , ARG A:8 , HIS A:49 , GLU A:108 , PHE A:135 , ACT A:801BINDING SITE FOR RESIDUE SO4 A 4770
03AC3SOFTWARETYR B:106 , MET B:153 , GLU B:175 , SO4 B:4771 , HOH B:4789BINDING SITE FOR RESIDUE ACT B 802
04AC4SOFTWAREHIS B:7 , ARG B:8 , HIS B:49 , GLU B:108 , ACT B:802BINDING SITE FOR RESIDUE SO4 B 4771
05AC5SOFTWARETYR C:106 , GLU C:108 , MET C:153 , GLU C:175 , SO4 C:4772BINDING SITE FOR RESIDUE ACT C 803
06AC6SOFTWAREHIS C:7 , ARG C:8 , HIS C:49 , ACT C:803BINDING SITE FOR RESIDUE SO4 C 4772
07AC7SOFTWARETYR D:106 , GLU D:108 , GLU D:175 , ASN D:221BINDING SITE FOR RESIDUE ACT D 804
08AC8SOFTWAREHIS D:7 , ARG D:8 , HIS D:49 , GLU D:108 , LYS D:110BINDING SITE FOR RESIDUE SO4 D 4773
09AC9SOFTWAREGLU E:34 , TYR E:106 , GLU E:108 , GLU E:175 , ASN E:221 , SO4 E:4774BINDING SITE FOR RESIDUE ACT E 805
10BC1SOFTWAREHIS E:7 , ARG E:8 , HIS E:49 , ACT E:805BINDING SITE FOR RESIDUE SO4 E 4774
11BC2SOFTWAREGLU F:34 , TYR F:106 , GLU F:108 , MET F:153 , GLU F:175 , ASN F:221 , SO4 F:4775BINDING SITE FOR RESIDUE ACT F 806
12BC3SOFTWAREHIS F:7 , ARG F:8 , TYR F:200 , ACT F:806BINDING SITE FOR RESIDUE SO4 F 4775

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ZCC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZCC)

(-) Exons   (0, 0)

(no "Exon" information available for 1ZCC)

(-) 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:240
 aligned with A9CG82_AGRFC | A9CG82 from UniProtKB/TrEMBL  Length:248

    Alignment length:240
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
         A9CG82_AGRFC     1 MTKIVSHRGANRFAPENTFAAADLALQQGADYIELDVRESADGVLYVIHDETLDRTTNGTGPVGHMLSSEIDTLDAGGWFDDRFKGAIVPRLDAYLEHLRGRAGVYIELKYCDPAKVAALVRHLGMVRDTFYFSFSEEMRQGLQSIAPEFRRMMTLDIAKSPSLVGAVHHASIIEITPAQMRRPGIIEASRKAGLEIMVYYGGDDMAVHREIATSDVDYINLDRPDLFAAVRSGMAELLL 240
               SCOP domains d1zcca1 A:1-240 Glycerophosphodiester phosphodiesterase UgpQ                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...........hhhhhhhhhhh...eeeeeeee.....eee...................hhhhhh........hhhhh.....hhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhh....eeee..hhhhhhhhhhhh...eeeeehhhhh..hhhhhh....eeeehhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1zcc A   1 MTKIVSHRGANRFAPENTFAAADLALQQGADYIELDVRESADGVLYVIHDETLDRTTNGTGPVGHMLSSEIDTLDAGGWFDDRFKGAIVPRLDAYLEHLRGRAGVYIELKYCDPAKVAALVRHLGMVRDTFYFSFSEEMRQGLQSIAPEFRRMMTLDIAKSPSLVGAVHHASIIEITPAQMRRPGIIEASRKAGLEIMVYYGGDDMAVHREIATSDVDYINLDRPDLFAAVRSGMAELLL 240
                                    10        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:228
 aligned with A9CG82_AGRFC | A9CG82 from UniProtKB/TrEMBL  Length:248

    Alignment length:230
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
         A9CG82_AGRFC     1 MTKIVSHRGANRFAPENTFAAADLALQQGADYIELDVRESADGVLYVIHDETLDRTTNGTGPVGHMLSSEIDTLDAGGWFDDRFKGAIVPRLDAYLEHLRGRAGVYIELKYCDPAKVAALVRHLGMVRDTFYFSFSEEMRQGLQSIAPEFRRMMTLDIAKSPSLVGAVHHASIIEITPAQMRRPGIIEASRKAGLEIMVYYGGDDMAVHREIATSDVDYINLDRPDLFAA 230
               SCOP domains d1zccb_ B: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...........hhhhhhhhhhh...eeeeeeee.....eee.....hhhhh....hhhhhhhhhhhhh......--........hhhhhhhhhh...eeeeeeee.hhhhhhhhhhhh.....eeee..hhhhhhhhhhhh...eeeeehhhhhhhhhhh......eeeehhhhhhh.hhhhhhhhh..eeeeee...hhhhhhhhhhh...eeee.hhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zcc B   1 MTKIVSHRGANRFAPENTFAAADLALQQGADYIELDVRESADGVLYVIHDETLDRTTNGTGPVGHMLSSEIDTLDAGGWF--RFKGAIVPRLDAYLEHLRGRAGVYIELKYCDPAKVAALVRHLGMVRDTFYFSFSEEMRQGLQSIAPEFRRMMTLDIAKSPSLVGAVHHASIIEITPAQMRRPGIIEASRKAGLEIMVYYGGDDMAVHREIATSDVDYINLDRPDLFAA 230
                                    10        20        30        40        50        60        70        80  |     90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
                                                                                                          80 83                                                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:233
 aligned with A9CG82_AGRFC | A9CG82 from UniProtKB/TrEMBL  Length:248

    Alignment length:234
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    
         A9CG82_AGRFC     1 MTKIVSHRGANRFAPENTFAAADLALQQGADYIELDVRESADGVLYVIHDETLDRTTNGTGPVGHMLSSEIDTLDAGGWFDDRFKGAIVPRLDAYLEHLRGRAGVYIELKYCDPAKVAALVRHLGMVRDTFYFSFSEEMRQGLQSIAPEFRRMMTLDIAKSPSLVGAVHHASIIEITPAQMRRPGIIEASRKAGLEIMVYYGGDDMAVHREIATSDVDYINLDRPDLFAAVRSG 234
               SCOP domains d1zccc_ C: automated matches                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..........hhhhhhhhhhh...eeeeeeee.....eee.....hhhhh....hhhhhhhhhhh............-.....hhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhh....eeee..hhhhhhhhhhhh...eeeeehhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhh...eeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1zcc C   1 MTKIVSHRGANRFAPENTFAAADLALQQGADYIELDVRESADGVLYVIHDETLDRTTNGTGPVGHMLSSEIDTLDAGGWFDDRF-GAIVPRLDAYLEHLRGRAGVYIELKYCDPAKVAALVRHLGMVRDTFYFSFSEEMRQGLQSIAPEFRRMMTLDIAKSPSLVGAVHHASIIEITPAQMRRPGIIEASRKAGLEIMVYYGGDDMAVHREIATSDVDYINLDRPDLFAAVRSG 234
                                    10        20        30        40        50        60        70        80   | |  90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    
                                                                                                              84 |                                                                                                                                                    
                                                                                                                86                                                                                                                                                    


Chain D from PDB  Type:PROTEIN  Length:231
 aligned with A9CG82_AGRFC | A9CG82 from UniProtKB/TrEMBL  Length:248

    Alignment length:231
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 
         A9CG82_AGRFC     1 MTKIVSHRGANRFAPENTFAAADLALQQGADYIELDVRESADGVLYVIHDETLDRTTNGTGPVGHMLSSEIDTLDAGGWFDDRFKGAIVPRLDAYLEHLRGRAGVYIELKYCDPAKVAALVRHLGMVRDTFYFSFSEEMRQGLQSIAPEFRRMMTLDIAKSPSLVGAVHHASIIEITPAQMRRPGIIEASRKAGLEIMVYYGGDDMAVHREIATSDVDYINLDRPDLFAAV 231
               SCOP domains d1zccd_ D: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...........hhhhhhhhhhh...eeeeeeee.....eee..............hhhhhhhhhhh..................hhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhh....eeee..hhhhhhhhhhhh...eeeeehhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhh...eeee.hhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zcc D   1 MTKIVSHRGANRFAPENTFAAADLALQQGADYIELDVRESADGVLYVIHDETLDRTTNGTGPVGHMLSSEIDTLDAGGWFDDRFKGAIVPRLDAYLEHLRGRAGVYIELKYCDPAKVAALVRHLGMVRDTFYFSFSEEMRQGLQSIAPEFRRMMTLDIAKSPSLVGAVHHASIIEITPAQMRRPGIIEASRKAGLEIMVYYGGDDMAVHREIATSDVDYINLDRPDLFAAV 231
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 


Chain E from PDB  Type:PROTEIN  Length:233
 aligned with A9CG82_AGRFC | A9CG82 from UniProtKB/TrEMBL  Length:248

    Alignment length:233
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   
         A9CG82_AGRFC     1 MTKIVSHRGANRFAPENTFAAADLALQQGADYIELDVRESADGVLYVIHDETLDRTTNGTGPVGHMLSSEIDTLDAGGWFDDRFKGAIVPRLDAYLEHLRGRAGVYIELKYCDPAKVAALVRHLGMVRDTFYFSFSEEMRQGLQSIAPEFRRMMTLDIAKSPSLVGAVHHASIIEITPAQMRRPGIIEASRKAGLEIMVYYGGDDMAVHREIATSDVDYINLDRPDLFAAVRS 233
               SCOP domains d1zcce_ E: automated matches                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...........hhhhhhhhhhh...eeeeeeee.....eee..............hhhhhhhhhhhh.......hhhhh.....hhhhhhhhhh...eeeeeeee.hhhhhhhhhhhh.....eeee..hhhhhhhhhhhh...eeeeehhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhh....eeee.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zcc E   1 MTKIVSHRGANRFAPENTFAAADLALQQGADYIELDVRESADGVLYVIHDETLDRTTNGTGPVGHMLSSEIDTLDAGGWFDDRFKGAIVPRLDAYLEHLRGRAGVYIELKYCDPAKVAALVRHLGMVRDTFYFSFSEEMRQGLQSIAPEFRRMMTLDIAKSPSLVGAVHHASIIEITPAQMRRPGIIEASRKAGLEIMVYYGGDDMAVHREIATSDVDYINLDRPDLFAAVRS 233
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   


Chain F from PDB  Type:PROTEIN  Length:235
 aligned with A9CG82_AGRFC | A9CG82 from UniProtKB/TrEMBL  Length:248

    Alignment length:235
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230     
         A9CG82_AGRFC     1 MTKIVSHRGANRFAPENTFAAADLALQQGADYIELDVRESADGVLYVIHDETLDRTTNGTGPVGHMLSSEIDTLDAGGWFDDRFKGAIVPRLDAYLEHLRGRAGVYIELKYCDPAKVAALVRHLGMVRDTFYFSFSEEMRQGLQSIAPEFRRMMTLDIAKSPSLVGAVHHASIIEITPAQMRRPGIIEASRKAGLEIMVYYGGDDMAVHREIATSDVDYINLDRPDLFAAVRSGM 235
               SCOP domains d1zccf_ F: automated matches                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...........hhhhhhhhhhhh..eeeeeeee.....eee.....hhhhh....hhhhhhhhhhh........hhhhh.....hhhhhhhhhh...eeeeee...hhhhhhhhhhhh.....eeee..hhhhhhhhhhhh...eeeeehhhhhhhhhh.......eeeehhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh...eeee.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zcc F   1 MTKIVSHRGANRFAPENTFAAADLALQQGADYIELDVRESADGVLYVIHDETLDRTTNGTGPVGHMLSSEIDTLDAGGWFDDRFKGAIVPRLDAYLEHLRGRAGVYIELKYCDPAKVAALVRHLGMVRDTFYFSFSEEMRQGLQSIAPEFRRMMTLDIAKSPSLVGAVHHASIIEITPAQMRRPGIIEASRKAGLEIMVYYGGDDMAVHREIATSDVDYINLDRPDLFAAVRSGM 235
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
   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  (2, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ZCC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1ZCC)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (A9CG82_AGRFC | A9CG82)
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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