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(-) Description

Title :  CRYSTAL STRUCTURE OF DIELS-ALDERASE CE20 IN COMPLEX WITH A PRODUCT ANALOG
 
Authors :  T. Beck, N. Preiswerk, C. Mayer, D. Hilvert
Date :  20 Dec 13  (Deposition) - 04 Jun 14  (Release) - 04 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Protein Engineering, Computer-Aided Design, Diels-Alder Reaction, Enzyme Design, Directed Evolution, Substrate Specificity, Beta- Propeller, Helix-Loop-Helix, De Novo Protein, Artificial Catalyst, Diels-Alderase, Catalyst For Cycloaddition, Hydrolase, Enzyme- Product Analog Complex' (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Preiswerk, T. Beck, J. D. Schulz, P. Milovnik, C. Mayer, J. B. Siegel D. Baker, D. Hilvert
Impact Of Scaffold Rigidity On The Design And Evolution Of An Artificial Diels-Alderase
Proc. Natl. Acad. Sci. Usa 2014
PubMed-ID: 24847076  |  Reference-DOI: 10.1073/PNAS.1401073111

(-) Compounds

Molecule 1 - DIISOPROPYL-FLUOROPHOSPHATASE
    Chains: A, B
    EC Number: 3.1.8.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Common: COMMON EUROPEAN SQUID
    Organism Scientific: LOLIGO VULGARIS
    Organism Taxid: 6622
    Synonym: DIELS-ALDERASE C20, DFPASE

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1XDA2Ligand/Ion4-{[2-(PHOSPHONOOXY)ETHYL]CARBAMOYL}BENZYL [(1R,6S)-6-(DIMETHYLCARBAMOYL)CYCLOHEX-2-EN-1-YL]CARBAMATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1XDA1Ligand/Ion4-{[2-(PHOSPHONOOXY)ETHYL]CARBAMOYL}BENZYL [(1R,6S)-6-(DIMETHYLCARBAMOYL)CYCLOHEX-2-EN-1-YL]CARBAMATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1XDA1Ligand/Ion4-{[2-(PHOSPHONOOXY)ETHYL]CARBAMOYL}BENZYL [(1R,6S)-6-(DIMETHYLCARBAMOYL)CYCLOHEX-2-EN-1-YL]CARBAMATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:42 , ALA A:45 , TYR A:134 , LEU A:161 , CYS A:186 , GLN A:208 , GLY A:235 , THR A:236 , LYS A:238 , TRP A:257BINDING SITE FOR RESIDUE XDA A 400
2AC2SOFTWAREALA B:45 , ASN B:46 , TYR B:134 , ILE B:159 , LEU B:161 , GLN B:208 , LYS B:238 , TRP B:257BINDING SITE FOR RESIDUE XDA B 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4O5T)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:153 -Pro A:154
2Ala B:153 -Pro B:154

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O5T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O5T)

(-) Exons   (0, 0)

(no "Exon" information available for 4O5T)

(-) 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:319
                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....eeee......eeeee.....eeee.hhhhhhhhhh............eeee......eeeee..ee..ee..eeeeee.....eeeeee...eeeeee....eee................eee.....eeeee..................eeeeee.....eeeeeeee..eeeeeeee.....eeeeeeee....eeeeeeeee..eeeeeeeeee.......eeeeeee.....eeeeee...eeeee........eeee.....eeeeee.....eeeeee....eeeeee.......hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o5t A   3 IPVIEPLFTKMTEDIPGATGPVFDKNGDFYVVASPLSEALINANSLAEARSDAGEILHIDLKTGKKTVICKPEVNGYGGSPIGCQCDRDANQLFVADMRLGLLVVQTDGTFEEIANKDSEGRCMQGCAYCAFDYEGNLWITAPAGGVAPADFTISLREKFGSIYCFTTDGQMIQVDTAFQCPAGIAVRHMNDGRPYQLIVAEQPTKKLWSYDIKGPANIENKKVWGHIPGTHKGGAAGMVFDEDNNLLVANWGSSHIEVFGPDGGQPKMRIRCPFEKPANLHFKPQTKTIFVTEHDNNAVWKFEWQRNGKKQYCETSKF 324
                                    12        22        32        42       |55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315         
                                                                          50|                                                                                                                                                                                                                                                                              
                                                                           54                                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee......eeeee.....eeeeehhhhhhhhhh.hhhhhh....eeeee......eeeee..ee..ee..eeeeee.....eeeeee...eeeeee....eee................eee.....eeeee..................eeeeee.....eeeeeeee..eeeeeeee.....eeeeeeee....eeeeeeeee..eeeeeeeeee.......eeeeeee.....eeeeee...eeeee........eeee.....eeeeee.....eeeeee....eeeeee.......hhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o5t B   2 EIPVIEPLFTKMTEDIPGATGPVFDKNGDFYVVASPLSEALINANSLAEAYSDAGEILHIDLKTGKKTVICKPEVNGYGGSPIGCQCDRDANQLFVADMRLGLLVVQTDGTFEEIANKDSEGRCMQGCAYCAFDYEGNLWITAPAGGVAPADFTISLREKFGSIYCFTTDGQMIQVDTAFQCPAGIAVRHMNDGRPYQLIVAEQPTKKLWSYDIKGPANIENKKVWGHIPGTHKGGAAGMVFDEDNNLLVANWGSSHIEVFGPDGGQPKMRIRCPFEKPANLHFKPQTKTIFVTEHDNNAVWKFEWQRNGKKQYCETSKFGIFGSL 330
                                    11        21        31        41        51||      64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324      
                                                                             52|                                                                                                                                                                                                                                                                                  
                                                                              56
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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  (0, 0)

(no "SCOP Domain" information available for 4O5T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O5T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O5T)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DFPA_LOLVU | Q7SIG4: 1e1a 1pjx 2gvu 2gvv 2gvw 2gvx 2iao 2iap 2iaq 2iar 2ias 2iat 2iau 2iav 2iaw 2iax 3byc 3hlh 3hli 3i1c 3kgg 3li3 3li4 3li5 3o4p 3u0s 4o5s

(-) Related Entries Specified in the PDB File

1e1a SCAFFOLD PROTEIN
3i1c DIELS-ALDERASE CE6
3u0s DIELS-ALDERASE DA 20.00
4o5s