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(-) Description

Title :  CRYSTAL STRUCTURE OF A DE NOVO RETRO-ALDOLASE CATALYZING ASYMMETRIC MICHAEL ADDITIONS, WITH A COVALENTLY BOUND PRODUCT ANALOG
 
Authors :  T. Beck, X. Garrabou Pi, D. Hilvert
Date :  07 Apr 14  (Deposition) - 01 Apr 15  (Release) - 13 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Engineering, Computer-Aided Design, Aldolase, Retro-Aldolase, Michael Addition, Enzyme Design, Directed Evolution, Substrate Specificity, De Novo Protein, Artificial Catalyst, Enzyme-Product Analog Complex, Tim-Barrel Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Garrabou, T. Beck, D. Hilvert
A Promiscuous De Novo Retro-Aldolase Catalyzes Asymmetric Michael Additions Via Schiff Base Intermediates.
Angew. Chem. Int. Ed. Engl. V. 54 5609 2015
PubMed-ID: 25777153  |  Reference-DOI: 10.1002/ANIE.201500217

(-) Compounds

Molecule 1 - RETRO-ALDOLASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
12K61Ligand/Ion(3R)-3-(4-METHOXYPHENYL)-5-OXOHEXANENITRILE
2GOL2Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:1027 , ARG A:1028 , PRO A:1029 , LYS A:1083 , PHE A:1089 , ASN A:1110 , ILE A:1133 , ASN A:1135 , LEU A:1159 , HOH A:2208binding site for residue 2K6 A 2001
2AC2SOFTWARETYR A:1051 , SER A:1235 , LEU A:1236 , MET A:1237 , ARG A:1238 , HOH A:2106 , HOH A:2115 , HOH A:2116binding site for residue SO4 A 2002
3AC3SOFTWAREASP A:1162 , GLU A:1163 , ASN A:1193 , LYS A:1196 , HOH A:2216 , HOH A:2265 , HOH A:2306 , HOH A:2349binding site for residue SO4 A 2003
4AC4SOFTWAREARG A:1036 , ARG A:1043 , HOH A:2117 , HOH A:2172 , HOH A:2344binding site for residue GOL A 2004
5AC5SOFTWAREGLU A:1116 , GLU A:1141 , HOH A:2141 , HOH A:2167 , HOH A:2348binding site for residue GOL A 2005

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PA8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PA8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 4PA8)

(-) 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    
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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:236
                                                                                                                                                                                                                                                                             
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh.............hhhhhhhhhhhhh...eeeee....hhhhhhhhhhh...eeeee........hhhhhhhhhhhh...eeee....hhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhh...eeee........hhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhh...eee.........hhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4pa8 A 1002 PRYLKGWLEDVVQLSLRRPSVHASRQRPIISLNERILEFNKRNITAIIAYYLRKRDPIEYAKYMERYAVGLSIKTEEKYFNGSYEMLRKIASSVSIPILMNDFIVKESQIDDAYNLGADTVLLIVNILTERELESLLEYARSYGMEPLILINDENDLDIALRIGARFIVIFSMNFGEINKENQRKLISMIPSNVVKVAHLDISERNEIEELRKLGVNAFLISSSLMRNPEKIKELI 1247
                                  1011      1021      1031      1041      1051   || 1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1169      1179    ||1191      1201      1211      1221      1231      1241      
                                                                              1055|                                                                                                                    1184|                                                            
                                                                               1064                                                                                                                     1187
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4PA8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PA8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PA8)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4PA8)

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 Related Entries

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(-) Related Entries Specified in the PDB File

4a29 STRUCTURE OF THE ENGINEERED RETRO-ALDOLASE RA95.0, EARLIER VARIANT OF RELATED ENZYME
4a2r STRUCTURE OF THE ENGINEERED RETRO-ALDOLASE RA95.5-5 , EARLIER VARIANT OF RELATED ENZYME
4a2s STRUCTURE OF THE ENGINEERED RETRO-ALDOLASE RA95.5, EARLIER VARIANT OF RELATED ENZYME