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(-) Description

Title :  STRUCTURE OF THE D55N MUTANT OF PHOSPHOLIPASE C FROM BACILLUS CEREUS
 
Authors :  N. M. Antikainen, A. F. Monzingo, C. L. Franklin, J. D. Robertus, S. F. Martin
Date :  28 Apr 03  (Deposition) - 30 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Tri Zn2+ Metal Core, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. M. Antikainen, A. F. Monzingo, C. L. Franklin, J. D. Robertus, S. F. Martin
Using X-Ray Crystallography Of The Asp55Asn Mutant Of The Phosphatidylcholine-Preferring Phospholipase C From Bacillus Cereus To Support The Mechanistic Role Of Asp55 As The General Base.
Arch. Biochem. Biophys. V. 417 81 2003
PubMed-ID: 12921783  |  Reference-DOI: 10.1016/S0003-9861(03)00343-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOLIPASE C
    Chains: A
    EC Number: 3.1.4.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL-C2
    Expression System Strain: DH5-ALPHA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PLC
    Mutation: YES
    Organism Scientific: BACILLUS CEREUS
    Organism Taxid: 1396
    Synonym: PLC, PHOSPHATIDYLCHOLINE CHOLINEPHOSPHOHYDROLASE, CEREOLYSIN A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1ZN3Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:55 , HIS A:69 , HIS A:118 , ASP A:122 , ZN A:248 , HOH A:249 , HOH A:452BINDING SITE FOR RESIDUE ZN A 246
2AC2SOFTWAREHIS A:128 , HIS A:142 , GLU A:146 , HOH A:250BINDING SITE FOR RESIDUE ZN A 247
3AC3SOFTWARETRP A:1 , HIS A:14 , ASP A:122 , ZN A:246 , HOH A:249BINDING SITE FOR RESIDUE ZN A 248

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P5X)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:58 -Pro A:59
2Tyr A:137 -Pro A:138

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_PHLC_BACCE_001 *E212DPHLC_BACCE  ---  ---AE174D
2UniProtVAR_PHLC_BACCE_002 *S226APHLC_BACCE  ---  ---AS188A
3UniProtVAR_PHLC_BACCE_003 *K239RPHLC_BACCE  ---  ---AK201R
4UniProtVAR_PHLC_BACCE_004 *D282NPHLC_BACCE  ---  ---AD244N
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROKAR_ZN_DEPEND_PLPC_1PS00384 Prokaryotic zinc-dependent phospholipase C signature.PHLC_BACCE156-169  1A:118-131

(-) Exons   (0, 0)

(no "Exon" information available for 1P5X)

(-) 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:245
 aligned with PHLC_BACCE | P09598 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:245
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278     
           PHLC_BACCE    39 WSAEDKHKEGVNSHLWIVNRAIDIMSRNTTLVKQDRVAQLNEWRTELENGIYAADYENPYYDNSTFASHFYDPDNGKTYIPFAKQAKETGAKYFKLAGESYKNKDMKQAFFYLGLSLHYLGDVNQPMHAANFTNLSYPQGFHSKYENFVDTIKDNYKVTDGNGYWNWKGTNPEEWIHGAAVVAKQDYSGIVNDNTKDWFVKAAVSQEYADKWRAEVTPMTGKRLMDAQRVTAGYIQLWFDTYGDR 283
               SCOP domains d1p5xa_ A: Bacterial phosholipase C                                                                                                                                                                                                                   SCOP domains
               CATH domains 1p5xA00 A:1-245 P1 Nuclease                                                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...........hhhhh..............hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------D-------------A------------R------------------------------------------N- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------PROKAR_ZN_DEPE------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p5x A   1 WSAEDKHKEGVNSHLWIVNRAIDIMSRNTTLVKQDRVAQLNEWRTELENGIYAANYENPYYDNSTFASHFYDPDNGKTYIPFAKQAKETGAKYFKLAGESYKNKDMKQAFFYLGLSLHYLGDVNQPMHAANFTNLSYPQGFHSKYENFVDTIKDNYKVTDGNGYWNWKGTNPEEWIHGAAVVAKQDYSGIVNDNTKDWFVKAAVSQEYADKWRAEVTPMTGKRLMDAQRVTAGYIQLWFDTYGDR 245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1P5X)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PHLC_BACCE | P09598)
molecular function
    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:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0034480    phosphatidylcholine phospholipase C activity    Catalysis of the reaction: phosphatidylcholine + H2O = 1,2-diacylglycerol + a choline phosphate.
    GO:0004629    phospholipase C activity    Catalysis of the reaction: a phospholipid + H2O = 1,2-diacylglycerol + a phosphatidate.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0044179    hemolysis in other organism    The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in one organism by another.

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  3.1.4.3
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 Related Entries

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

UniProtKB/Swiss-Prot
        PHLC_BACCE | P09598: 1ah7 1p6d 1p6e 2ffz 2fgn 2huc

(-) Related Entries Specified in the PDB File

1ah7 PHOSPHOLIPASE C FROM BACILLUS CEREUS
1p6d PHOSPHOLIPASE C FROM BACILLUS CEREUS IN COMPLEX WITH (3S)- 3,4-DI-N-HEXANOYLOXYBUTYL-1-PHOSPHOCHOLINE
1p6e THE D55N MUTANT OF PHOSPHOLIPASE C FROM BACILLUS CEREUS WITH 1,2-DI-N-PENTANOYL-SN-GLYCERO-3-DITHIOPHOSPHOCHOLINE