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(-) Description

Title :  MALONATE-BOUND STRUCTURE OF THE GLYCEROPHOSPHODIESTERASE FROM ENTEROBACTER AEROGENES (GPDQ) COLLECTED AT 1.280 ANGSTROM
 
Authors :  D. L. Ollis, C. J. Jackson, P. D. Carr
Date :  07 May 08  (Deposition) - 07 Oct 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Malonate, Metalloenzyme, Iron, Phosphodiesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. J. Jackson, K. S. Hadler, P. D. Carr, A. J. Oakley, S. Yip, G. Schenk, D. L. Ollis
Malonate-Bound Structure Of The Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) And Characterization Of The Native Fe2+ Metal-Ion Preference.
Acta Crystallogr. , Sect. F V. 64 681 2008
PubMed-ID: 18678932  |  Reference-DOI: 10.1107/S1744309108017600

(-) Compounds

Molecule 1 - PHOSPHOHYDROLASE
    Chains: A, B
    EC Number: 3.1.4.46
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCY76
    Expression System Strain: DH5A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GPDQ
    Organism Scientific: ENTEROBACTER AEROGENES
    Organism Taxid: 548
    Synonym: GPDQ, GLYCEROPHOSPHODIESTERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB
Biological Unit 2 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1FE24Ligand/IonFE (II) ION
2MLI2Ligand/IonMALONATE ION
Biological Unit 1 (2, 18)
No.NameCountTypeFull Name
1FE212Ligand/IonFE (II) ION
2MLI6Ligand/IonMALONATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1FE24Ligand/IonFE (II) ION
2MLI2Ligand/IonMALONATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:8 , HIS A:10 , ASP A:50 , HIS A:197BINDING SITE FOR RESIDUE FE2 A 275
2AC2SOFTWAREASP A:50 , ASN A:80 , HIS A:156 , HIS A:195BINDING SITE FOR RESIDUE FE2 A 276
3AC3SOFTWAREASP B:8 , HIS B:10 , ASP B:50 , HIS B:197BINDING SITE FOR RESIDUE FE2 B 275
4AC4SOFTWAREASP B:50 , ASN B:80 , HIS B:156 , HIS B:195BINDING SITE FOR RESIDUE FE2 B 276
5AC5SOFTWAREASP A:8 , HIS A:10 , ASP A:50 , ASN A:80 , HIS A:81 , HIS A:195 , HIS A:197BINDING SITE FOR RESIDUE MLI A 277
6AC6SOFTWAREHIS B:10 , ASP B:50 , ASN B:80 , HIS B:81 , HIS B:195 , HIS B:197BINDING SITE FOR RESIDUE MLI B 277

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:54 -B:269
2A:269 -B:54

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:259 -Pro A:260
2Gly B:259 -Pro B:260

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ZOA)

(-) 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:271
 aligned with Q6XBH1_ENTAE | Q6XBH1 from UniProtKB/TrEMBL  Length:274

    Alignment length:271
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270 
         Q6XBH1_ENTAE     1 MLLAHISDTHFRSRGEKLYGFIDVNAANADVVSQLNALRERPDAVVVSGDIVNCGRPEEYQVARQILGSLNYPLYLIPGNHDDKALFLEYLQPLCPQLGSDANNMRCAVDDFATRLLFIDSSRAGTSKGWLTDETISWLEAQLFEGGDKPATIFMHHPPLPLGNAQMDPIACENGHRLLALVERFPSLTRIFCGHNHSLTMTQYRQALISTLPGTVHQVPYCHEDTRPYYDLSPASCLMHRQVGEQWVSYQHSLAHYAGPWLYDENISCPT 271
               SCOP domains d2zoaa_ A: Glycerophosphodiesterase GpdQ                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..........hhhhh.hhhhhhhhhhhhhhhh.....eeee........hhhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhhhh......eeee.....eeeee............hhhhhhhhhhhhhh.....eeeee...........hhhhh...hhhhhhhhhhh..eeeeee......eeeee..eeeee.................eeee...eeeeeeee..eeeeeeee.......ee.hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zoa A   1 MLLAHISDTHFRSRGEKLYGFIDVNAANADVVSQLNALRERPDAVVVSGDIVNCGRPEEYQVARQILGSLNYPLYLIPGNHDDKALFLEYLQPLCPQLGSDANNMRCAVDDFATRLLFIDSSRAGTSKGWLTDETISWLEAQLFEGGDKPATIFMHHPPLPLGNAQMDPIACENGHRLLALVERFPSLTRIFCGHNHSLTMTQYRQALISTLPGTVHQVPYCHADTDPYYDLSPASCLMHRQVGEQWVSYQHSLAHYAGPWLYDENISCPT 271
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270 


Chain B from PDB  Type:PROTEIN  Length:271
 aligned with Q6XBH1_ENTAE | Q6XBH1 from UniProtKB/TrEMBL  Length:274

    Alignment length:271
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270 
         Q6XBH1_ENTAE     1 MLLAHISDTHFRSRGEKLYGFIDVNAANADVVSQLNALRERPDAVVVSGDIVNCGRPEEYQVARQILGSLNYPLYLIPGNHDDKALFLEYLQPLCPQLGSDANNMRCAVDDFATRLLFIDSSRAGTSKGWLTDETISWLEAQLFEGGDKPATIFMHHPPLPLGNAQMDPIACENGHRLLALVERFPSLTRIFCGHNHSLTMTQYRQALISTLPGTVHQVPYCHEDTRPYYDLSPASCLMHRQVGEQWVSYQHSLAHYAGPWLYDENISCPT 271
               SCOP domains d2zoab_ B: Glycerophosphodiesterase GpdQ                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Metallophos-2zoaB01 B:1-199                                                                                                                                                                            ------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) Metallophos-2zoaB02 B:1-199                                                                                                                                                                            ------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author .eeeee..........hhhhh.hhhhhhhhhhhhhhhh.....eeeee.......hhhhhhhhhhhhhh....eeee.....hhhhhhhhhh..hhhhh.......eee.....eeee.............hhhhhhhhhhhhhhhh...eeee............hhhhh...hhhhhhhhhhh..eeeeee......eeeee..eeeee.................ee.....eeeeeeee..eeeeeeee....eeeee.hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zoa B   1 MLLAHISDTHFRSRGEKLYGFIDVNAANADVVSQLNALRERPDAVVVSGDIVNCGRPEEYQVARQILGSLNYPLYLIPGNHDDKALFLEYLQPLCPQLGSDANNMRCAVDDFATRLLFIDSSRAGTSKGWLTDETISWLEAQLFEGGDKPATIFMHHPPLPLGNAQMDPIACENGHRLLALVERFPSLTRIFCGHNHSLTMTQYRQALISTLPGTVHQVPYCHADTDPYYDLSPASCLMHRQVGEQWVSYQHSLAHYAGPWLYDENISCPT 271
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZOA)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Calcineurin (56)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q6XBH1_ENTAE | Q6XBH1)
molecular function
    GO:0004115    3',5'-cyclic-AMP phosphodiesterase activity    Catalysis of the reaction: adenosine 3',5'-cyclic phosphate + H2O = adenosine 5'-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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

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        Q6XBH1_ENTAE | Q6XBH1: 2dxl 2dxn 2zo9 3d03

(-) Related Entries Specified in the PDB File

2zo9 COLLECTED AT 1.295 ANGSTROM