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(-) Description

Title :  CYCLES OF DESTABILIZATION AND REPAIR UNDERLIE THE EVOLUTION OF NEW ENZYME FUNCTION
 
Authors :  C. J. Jackson, E. Campbell, M. Kaltenbach, N. Tokuriki
Date :  14 Dec 14  (Deposition) - 16 Dec 15  (Release) - 26 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,G
Keywords :  Dynamics, Evolution, Phosphotriesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Campbell, M. Kaltenbach, G. J. Correy, P. D. Carr, B. T. Porebski, E. K. Livingstone, L. Afriat-Jurnou, A. M. Buckle, M. Weik, F. Hollfelder, N. Tokuriki, C. J. Jackson
The Role Of Protein Dynamics In The Evolution Of New Enzyme Function.
Nat. Chem. Biol. V. 12 944 2016
PubMed-ID: 27618189  |  Reference-DOI: 10.1038/NCHEMBIO.2175

(-) Compounds

Molecule 1 - PHOSPHOTRIESTERASE VARIANT PTE-R6
    Chains: A, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BREVUNDIMONAS DIMINUTA
    Organism Taxid: 293

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1CAC1Ligand/IonCACODYLATE ION
2KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4ZN4Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:55 , HIS A:57 , KCX A:169 , ASP A:301 , ZN A:2402 , HOH A:2705binding site for residue ZN A 2401
2AC2SOFTWAREKCX A:169 , HIS A:201 , HIS A:230 , ZN A:2401 , MPD A:2404 , HOH A:2705binding site for residue ZN A 2402
3AC3SOFTWAREGLN A:343 , ALA A:347 , MPD A:2405binding site for residue MPD A 2403
4AC4SOFTWARELEU A:106 , ARG A:254 , HIS A:257 , LEU A:271 , ASP A:301 , ZN A:2402 , HOH A:2639 , HOH A:2705binding site for residue MPD A 2404
5AC5SOFTWAREPHE A:51 , GLY A:94 , LEU A:346 , ALA A:347 , THR A:350 , MPD A:2403 , HOH A:2552binding site for residue MPD A 2405
6AC6SOFTWAREHIS G:55 , TRP G:131 , KCX G:169 , HIS G:201 , HIS G:230 , ARG G:254 , ASP G:301 , ZN G:402 , ZN G:403 , HOH G:669 , HOH G:688binding site for residue CAC G 401
7AC7SOFTWAREHIS G:55 , HIS G:57 , KCX G:169 , ASP G:301 , CAC G:401 , ZN G:403binding site for residue ZN G 402
8AC8SOFTWAREKCX G:169 , HIS G:201 , HIS G:230 , CAC G:401 , ZN G:402 , HOH G:699binding site for residue ZN G 403
9AC9SOFTWAREPHE G:51 , GLN G:343binding site for residue MPD G 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XAG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XAG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XAG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XAG)

(-) Exons   (0, 0)

(no "Exon" information available for 4XAG)

(-) 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:329
                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.hhh..eeeee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhh.hhhhhhhhhhhhh.eee.eeee....hhhhhh.hhhhhhhhhhhhhhh..........eeeeeee...hhhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhh..hhh.eee.hhhhh.hhhhhhhhhhh..eeee.......................hhhhhhhhhhhhhhh.hhh.eee......ee.....hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xag A  34 GDRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDLGRDVSLLAEVSRAADVHIVAATGLWLDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIkVAITGKVTPFQELVLRAAARASLATGVPVTTHTAASQRGGEQQAAIFESEGLSPSRVCIGHSDETDDLSYLTALAARGYLIGLDRIPHSAIGLEDNASATALLGSRSWQTRALLIKALIDQGYMKQILVSNDWLFGLSSYVTNIMDVMDSVNPDGMAFIPLRVIPFLREKGIPQETLAGITVTNPARFLSPTL 362
                                    43        53        63        73        83        93       103       113       123       133       143       153       163     | 173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353         
                                                                                                                                                                 169-KCX                                                                                                                                                                                             


Chain G from PDB  Type:PROTEIN  Length:329
                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eeehhhhhh.eeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhh.hhhhhhhhhhhhh.eee.eeee....hhhhhh.hhhhhhhhhhhhhhh..........eeeee.....hhhhhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhh..hhh.eee.hhhhh.hhhhhhhhhhh..eeee............hhhhhhhhh..hhhhhhhhhhhhhhh.hhh.eee.............hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xag G  34 GDRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDLGRDVSLLAEVSRAADVHIVAATGLWLDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIkVAITGKVTPFQELVLRAAARASLATGVPVTTHTAASQRGGEQQAAIFESEGLSPSRVCIGHSDETDDLSYLTALAARGYLIGLDRIPHSAIGLEDNASATALLGSRSWQTRALLIKALIDQGYMKQILVSNDWLFGLSSYVTNIMDVMDSVNPDGMAFIPLRVIPFLREKGIPQETLAGITVTNPARFLSPTL 362
                                    43        53        63        73        83        93       103       113       123       133       143       153       163     | 173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353         
                                                                                                                                                                 169-KCX
   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 4XAG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XAG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XAG)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4XAG)

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 Related Entries

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(-) Related Entries Specified in the PDB File

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