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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LPQC, POLY(3-HYDROXYBUTYRATE) DEPOLYMERASE FROM BORDETELLA PARAPERTUSSIS
 
Authors :  Y. Kim, C. Tesar, R. Jedrzejczak, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  01 May 08  (Deposition) - 01 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha-Beta-Alpha Sandwich, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, C. Tesar, R. Jedrzejczak, A. Joachimiak
Crystal Structure Of The Lpqc, Poly(3-Hydroxybutyrate) Depolymerase From Bordetella Parapertussis.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE POLY(3-HYDROXYBUTYRATE) DEPOLYMERASE LPQC
    Atcc: BAA-587
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19B
    Expression System Strain: BL21(DE3)
    Expression System Vector Type: PLASMID
    Gene: BPP4128
    Organism Scientific: BORDETELLA PARAPERTUSSIS 12822
    Organism Taxid: 257311
    Strain: 12822 / NCTC 13253

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 26)

Asymmetric Unit (4, 26)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2FMT3Ligand/IonFORMIC ACID
3MSE8Mod. Amino AcidSELENOMETHIONINE
4SO412Ligand/IonSULFATE ION
Biological Unit 1 (3, 11)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FMT1Ligand/IonFORMIC ACID
3MSE4Mod. Amino AcidSELENOMETHIONINE
4SO46Ligand/IonSULFATE ION
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FMT2Ligand/IonFORMIC ACID
3MSE4Mod. Amino AcidSELENOMETHIONINE
4SO46Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG B:111BINDING SITE FOR RESIDUE CL B 302
02AC2SOFTWARESER A:145 , ALA A:146 , GLN A:149 , GLY A:172 , PRO A:222 , ARG A:234BINDING SITE FOR RESIDUE SO4 A 304
03AC3SOFTWARESER B:145 , ALA B:146 , GLN B:149 , GLY B:172 , ASN B:220 , PRO B:222 , ARG B:234BINDING SITE FOR RESIDUE SO4 B 303
04AC4SOFTWAREGLY B:59 , TYR B:67 , HIS B:144 , SER B:145 , HIS B:268BINDING SITE FOR RESIDUE SO4 B 304
05AC5SOFTWARETHR A:105 , ALA A:107 , ASN A:109BINDING SITE FOR RESIDUE SO4 A 305
06AC6SOFTWARETYR B:45 , GLY B:46BINDING SITE FOR RESIDUE SO4 B 305
07AC7SOFTWAREGLY A:59 , TYR A:67 , HIS A:144 , SER A:145 , HIS A:268BINDING SITE FOR RESIDUE SO4 A 306
08AC8SOFTWAREARG A:21 , SER B:88 , ASP B:89 , GLU B:90BINDING SITE FOR RESIDUE SO4 B 306
09AC9SOFTWAREASP B:188 , GLY B:189 , GLY B:191BINDING SITE FOR RESIDUE SO4 B 307
10BC1SOFTWAREGLY B:94 , GLU B:96 , ARG B:285 , ASP B:288BINDING SITE FOR RESIDUE SO4 B 308
11BC2SOFTWAREHIS A:18 , ALA A:19 , TYR A:45BINDING SITE FOR RESIDUE SO4 A 307
12BC3SOFTWAREGLY A:94 , GLU A:96 , ARG A:285BINDING SITE FOR RESIDUE SO4 A 308
13BC4SOFTWAREASP A:288 , ALA A:289BINDING SITE FOR RESIDUE SO4 A 309
14BC5SOFTWAREASN A:63 , GLY A:64 , ALA A:65 , ASP A:66BINDING SITE FOR RESIDUE FMT A 310
15BC6SOFTWAREASN B:63 , GLY B:64 , ALA B:65 , ASP B:66BINDING SITE FOR RESIDUE FMT B 309
16BC7SOFTWAREALA B:33 , ASP B:34 , ARG B:35BINDING SITE FOR RESIDUE FMT B 310

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D0K)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:183 -Pro A:184
2Phe B:183 -Pro B:184

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D0K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D0K)

(-) Exons   (0, 0)

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(-) 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:287
 aligned with Q7W3B7_BORPA | Q7W3B7 from UniProtKB/TrEMBL  Length:301

    Alignment length:292
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294  
         Q7W3B7_BORPA     5 DLTNADRIALELGHAGRNAIPYLDDDRNADRPFTLNTYRPYGYTPDRPVVVVQHGVLRNGADYRDFWIPAADRHKLLIVAPTFSDEIWPGVESYNNGRAFTAAGNPRHVDGWTYALVARVLANIRAAEIADCEQVYLFGHSAGGQFVHRLMSSQPHAPFHAVTAANPGWYTLPTFEHRFPEGLDGVGLTEDHLARLLAYPMTILAGDQDIATDDPNLPSEPAALRQGPHRYARARHYYEAGQRAAAQRGLPFGWQLQVVPGIGHDGQAMSQVCASLWFDGRMPDAAELARLA 296
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3d0kA00 A:5-296  [code=3   .40.50.1820, no name defined]                                                                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh...eeeeeee..---.....eeeeeee.........eeeee.....hhhhhhhhhhhhhhhhh.eeeeee......hhhhhh.............hhhhhhhhhhhhhhhhhhhh.......eeeeeehhhhhhhhhhhhhh......eeeee.......................hhhhhhhhhhh..eeeee......--.....hhhhhh...hhhhhhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhhhh....hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d0k A   5 DLTNADRIALELGHAGRNAIPYLD---NADRPFTLNTYRPYGYTPDRPVVVVQHGVLRNGADYRDFWIPAADRHKLLIVAPTFSDEIWPGVESYNNGRAFTAAGNPRHVDGWTYALVARVLANIRAAEIADCEQVYLFGHSAGGQFVHRLmSSQPHAPFHAVTAANPGWYTLPTFEHRFPEGLDGVGLTEDHLARLLAYPmTILAGDQDIAT--PNLPSEPAALRQGPHRYARARHYYEAGQRAAAQRGLPFGWQLQVVPGIGHDGQAmSQVCASLWFDGRmPDAAELARLA 296
                                    14        24   |   |34        44        54        64        74        84        94       104       114       124       134       144       154|      164       174       184       194       204|      214 |  |  224       234       244       254       264       274       284 |     294  
                                                  28  32                                                                                                                        155-MSE                                           205-MSE    216  |                                                   273-MSE      286-MSE      
                                                                                                                                                                                                                                                219                                                                             


Chain B from PDB  Type:PROTEIN  Length:293
 aligned with Q7W3B7_BORPA | Q7W3B7 from UniProtKB/TrEMBL  Length:301

    Alignment length:295
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291     
         Q7W3B7_BORPA     2 KPADLTNADRIALELGHAGRNAIPYLDDDRNADRPFTLNTYRPYGYTPDRPVVVVQHGVLRNGADYRDFWIPAADRHKLLIVAPTFSDEIWPGVESYNNGRAFTAAGNPRHVDGWTYALVARVLANIRAAEIADCEQVYLFGHSAGGQFVHRLMSSQPHAPFHAVTAANPGWYTLPTFEHRFPEGLDGVGLTEDHLARLLAYPMTILAGDQDIATDDPNLPSEPAALRQGPHRYARARHYYEAGQRAAAQRGLPFGWQLQVVPGIGHDGQAMSQVCASLWFDGRMPDAAELARLA 296
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3d0kB00 B:2-296  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh...eeeeeee..........eeeeeee.........eeeee.....hhhhhhhhhhhhhhhhh.eeeeee......hhhhhh.............hhhhhhhhhhhhhhhhhhhh.......eeeeeehhhhhhhhhhhhhh......eeeee.......................hhhhhhhhhhh..eeeee......--.....hhhhhh...hhhhhhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhhhh....hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d0k B   2 KPADLTNADRIALELGHAGRNAIPYLDDDRNADRPFTLNTYRPYGYTPDRPVVVVQHGVLRNGADYRDFWIPAADRHKLLIVAPTFSDEIWPGVESYNNGRAFTAAGNPRHVDGWTYALVARVLANIRAAEIADCEQVYLFGHSAGGQFVHRLmSSQPHAPFHAVTAANPGWYTLPTFEHRFPEGLDGVGLTEDHLARLLAYPmTILAGDQDIAT--PNLPSEPAALRQGPHRYARARHYYEAGQRAAAQRGLPFGWQLQVVPGIGHDGQAmSQVCASLWFDGRmPDAAELARLA 296
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   |   161       171       181       191       201   |   211    |  221       231       241       251       261       271 |     281    |  291     
                                                                                                                                                                                   155-MSE                                           205-MSE    216  |                                                   273-MSE      286-MSE      
                                                                                                                                                                                                                                                   219
   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  (0, 0)

(no "SCOP Domain" information available for 3D0K)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D0K)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3D0K)

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