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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHORYLCHOLINE ESTERASE DOMAIN OF THE VIRULENCE FACTOR CHOLINE BINDING PROTEIN E FROM STREPTOCOCCUS PNEUMONIAE
 
Authors :  G. Garau, O. Dideberg
Date :  13 Oct 04  (Deposition) - 31 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A  (2x)
Keywords :  Phosphocholine, Iron, Esterase, Choline, Binding, Domain, Streptococcus, Pneum, Metallo, Lactamase, Pce, Cbpe, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Garau, D. Lemaire, T. Vernet, O. Dideberg, A. M. Di Guilmi
Crystal Structure Of Phosphorylcholine Esterase Domain Of The Virulence Factor Choline-Binding Protein E From Streptococcus Pneumoniae: New Structural Features Among The Metallo-Beta-Lactamase Superfamily
J. Biol. Chem. V. 280 28591 2005
PubMed-ID: 15908436  |  Reference-DOI: 10.1074/JBC.M502744200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TEICHOIC ACID PHOSPHORYLCHOLINE ESTERASE/CHOLINE BINDING PROTEIN E (CBPE)
    Chains: A, B
    EC Number: 3.1.4.38
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: CATALYTIC DOMAIN
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE R6
    Organism Taxid: 171101
    Strain: ATCC BAA-255 / R6

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 21)

Asymmetric Unit (4, 21)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2FE4Ligand/IonFE (III) ION
3MPD11Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4PC2Ligand/IonPHOSPHOCHOLINE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FE-1Ligand/IonFE (III) ION
3MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4PC-1Ligand/IonPHOSPHOCHOLINE
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FE-1Ligand/IonFE (III) ION
3MPD5Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4PC-1Ligand/IonPHOSPHOCHOLINE
Biological Unit 3 (1, 12)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FE-1Ligand/IonFE (III) ION
3MPD12Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4PC-1Ligand/IonPHOSPHOCHOLINE

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:110 , HIS A:112 , ASN A:208 , ASP A:228 , FE A:402 , PC A:501 , HOH A:508BINDING SITE FOR RESIDUE FE A 401
02AC2SOFTWAREASP A:114 , HIS A:115 , ASP A:228 , HIS A:254 , FE A:401 , PC A:501 , HOH A:508BINDING SITE FOR RESIDUE FE A 402
03AC3SOFTWAREASP A:62 , GLY A:117 , ASP A:120 , GLU A:121 , HOH A:526 , HOH A:528BINDING SITE FOR RESIDUE CA A 403
04AC4SOFTWAREGLU A:61 , ASP A:62 , ASP A:64 , HOH A:524 , HOH A:543 , HOH A:590BINDING SITE FOR RESIDUE CA A 404
05AC5SOFTWAREHIS B:110 , HIS B:112 , ASN B:208 , ASP B:228 , FE B:402 , PC B:501 , HOH B:1513BINDING SITE FOR RESIDUE FE B 401
06AC6SOFTWAREASP B:114 , HIS B:115 , ASP B:228 , HIS B:254 , FE B:401 , PC B:501 , HOH B:1513BINDING SITE FOR RESIDUE FE B 402
07AC7SOFTWAREGLU B:61 , ASP B:62 , ASP B:64 , HOH B:1514 , HOH B:1515 , HOH B:1516BINDING SITE FOR RESIDUE CA B 403
08AC8SOFTWAREASP B:62 , GLY B:117 , ASP B:120 , GLU B:121 , HOH B:1559 , HOH B:1560BINDING SITE FOR RESIDUE CA B 404
09AC9SOFTWAREGLY A:78 , HIS A:112 , ASP A:114 , TRP A:148 , ASN A:208 , ASP A:228 , HIS A:253 , HIS A:254 , FE A:401 , FE A:402 , HOH A:508 , HOH A:509 , HOH A:517BINDING SITE FOR RESIDUE PC A 501
10BC1SOFTWAREGLY B:78 , HIS B:112 , ASP B:114 , TRP B:148 , ASN B:208 , ASP B:228 , HIS B:253 , HIS B:254 , FE B:401 , FE B:402 , HOH B:1513 , HOH B:1521 , HOH B:1528BINDING SITE FOR RESIDUE PC B 501
11BC2SOFTWAREHIS A:255 , SER A:280 , TRP A:283BINDING SITE FOR RESIDUE MPD A 502
12BC3SOFTWAREGLN A:101 , THR A:125 , TYR A:126BINDING SITE FOR RESIDUE MPD A 503
13BC4SOFTWARETYR A:126 , PRO A:127 , THR A:164BINDING SITE FOR RESIDUE MPD A 505
14BC5SOFTWARETYR A:63 , ASP A:67 , MPD A:507BINDING SITE FOR RESIDUE MPD A 506
15BC6SOFTWARETYR A:63 , ASP A:67 , MPD A:506BINDING SITE FOR RESIDUE MPD A 507
16BC7SOFTWAREHIS B:255 , TRP B:283BINDING SITE FOR RESIDUE MPD B 1502
17BC8SOFTWARETHR B:125 , HOH B:1565BINDING SITE FOR RESIDUE MPD B 1503
18BC9SOFTWARELEU B:123 , TYR B:126 , THR B:164 , HOH B:1561BINDING SITE FOR RESIDUE MPD B 1504
19CC1SOFTWAREPHE B:92BINDING SITE FOR RESIDUE MPD B 1505
20CC2SOFTWAREASP B:67 , TRP B:75BINDING SITE FOR RESIDUE MPD B 1506

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Gly A:30 -Asn A:31
2Gln A:174 -Gly A:175
3Ser B:28 -Ser B:29
4Gln B:174 -Gly B:175
5Ser B:197 -Ser B:198
6Pro B:333 -Ser B:334

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WRA)

(-) 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:305
 aligned with Q8DQ62_STRR6 | Q8DQ62 from UniProtKB/TrEMBL  Length:627

    Alignment length:305
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329     
         Q8DQ62_STRR6    30 GNKIHFINVQEGGSDAIILESNGHFAMVDTGEDYDFPDGSDSRYPWREGIETSYKHVLTDRVFRRLKELSVQKLDFILVTHTHSDHIGNVDELLSTYPVDRVYLKKYSDSRITNSERLWDNLYGYDKVLQTATETGVSVIQNITQGDAHFQFGDMDIQLYNYENETDSSGELKKIWDDNSNSLISVVKVNGKKIYLGGDLDNVHGAEDKYGPLIGKVDLMKFNHHHDTNKSNTKDFIKNLSPSLIVQTSDSLPWKNGVDSEYVNWLKERGIERINAASKDYDATVFDIRKDGFVNISTSYKPIPS 334
               SCOP domains d1wraa1 A:30-334 Teichoic acid phosphorylcholine esterase Pce (LytD), N-terminal domain                                                                                                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........eeeeee..eeeeeee......................hhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhh...eeeee....hhhhh.hhhhh.hhhhhhhhhhhhhhhhh.eee........eeee..eeeeee................hhhhhh.eeeeee..eeeee........hhhhhhhhhhh...eee...........hhhhhhhhh..eeee...........hhhhhhhhhhh..eeee.......eeeeeee..eeee.hhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wra A  30 GNKIHFINVQEGGSDAIILESNGHFAMVDTGEDYDFPDGSDSRYPWREGIETSYKHVLTDRVFRRLKELSVQKLDFILVTHTHSDHIGNVDELLSTYPVDRVYLKKYSDSRITNSERLWDNLYGYDKVLQTATETGVSVIQNITQGDAHFQFGDMDIQLYNYENETDSSGELKKIWDDNSNSLISVVKVNGKKIYLGGDLDNVHGAEDKYGPLIGKVDLMKFNHHHDTNKSNTKDFIKNLSPSLIVQTSDSLPWKNGVDSEYVNWLKERGIERINAASKDYDATVFDIRKDGFVNISTSYKPIPS 334
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329     


Chain B from PDB  Type:PROTEIN  Length:308
 aligned with Q8DQ62_STRR6 | Q8DQ62 from UniProtKB/TrEMBL  Length:627

    Alignment length:308
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326        
         Q8DQ62_STRR6    27 ESSGNKIHFINVQEGGSDAIILESNGHFAMVDTGEDYDFPDGSDSRYPWREGIETSYKHVLTDRVFRRLKELSVQKLDFILVTHTHSDHIGNVDELLSTYPVDRVYLKKYSDSRITNSERLWDNLYGYDKVLQTATETGVSVIQNITQGDAHFQFGDMDIQLYNYENETDSSGELKKIWDDNSNSLISVVKVNGKKIYLGGDLDNVHGAEDKYGPLIGKVDLMKFNHHHDTNKSNTKDFIKNLSPSLIVQTSDSLPWKNGVDSEYVNWLKERGIERINAASKDYDATVFDIRKDGFVNISTSYKPIPS 334
               SCOP domains d1wrab_ B: Teichoic acid phosphorylcholine esterase Pce (LytD), N-terminal domain                                                                                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------Lactamase_B-1wraB01 B:38-300                                                                                                                                                                                                                                           ---------------------------------- Pfam domains (1)
           Pfam domains (2) -----------Lactamase_B-1wraB02 B:38-300                                                                                                                                                                                                                                           ---------------------------------- Pfam domains (2)
         Sec.struct. author ....eeeeee........eeeeee..eeeeeee......................hhhhhhhhhhhhhhhhh.......ee....hhhhhhhhhhhhh.....eee....hhhhh.hhhhh.hhhhhhhhhhhhhhhhh.eee........eeee..eeeeee................hhhhhh.eeeeee..eeeee........hhhhhhhhhhh...eee...........hhhhhhhhh..eeee...........hhhhhhhhhhh..eeee.......eeeeeee..eeee.hhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wra B  27 ESSGNKIHFINVQEGGSDAIILESNGHFAMVDTGEDYDFPDGSDSRYPWREGIETSYKHVLTDRVFRRLKELSVQKLDFILVTHTHSDHIGNVDELLSTYPVDRVYLKKYSDSRITNSERLWDNLYGYDKVLQTATETGVSVIQNITQGDAHFQFGDMDIQLYNYENETDSSGELKKIWDDNSNSLISVVKVNGKKIYLGGDLDNVHGAEDKYGPLIGKVDLMKFNHHHDTNKSNTKDFIKNLSPSLIVQTSDSLPWKNGVDSEYVNWLKERGIERINAASKDYDATVFDIRKDGFVNISTSYKPIPS 334
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326
   Legend:   → Mismatch (orange background)
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    → 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 1WRA)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Metallo-HOrase (67)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8DQ62_STRR6 | Q8DQ62)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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