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(-) Description

Title :  CRYSTAL STRUCTURE OF DIELS-ALDERASE PYRI4 IN COMPLEX WITH ITS PRODUCT
 
Authors :  L. Pan, Y. Guo, J. Liu
Date :  03 Jun 15  (Deposition) - 24 Feb 16  (Release) - 30 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Diels-Alderase, Complex, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Zheng, Y. Guo, L. Yang, Z. Zhao, Z. Wu, H. Zhang, J. Liu, X. Cheng, J. Wu H. Yang, H. Jiang, L. Pan, W. Liu
Enzyme-Dependent [4 + 2] Cycloaddition Depends On Lid-Like Interaction Of The N-Terminal Sequence With The Catalytic Core In Pyri4
Cell Chem Biol V. 23 352 2016
PubMed-ID: 26877021  |  Reference-DOI: 10.1016/J.CHEMBIOL.2016.01.005

(-) Compounds

Molecule 1 - PYRI4
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Plasmid: PET28A
    Expression System Strain: BL21-GOLD(DE3)PLYSS AG
    Expression System Taxid: 866768
    Expression System Vector Type: PLASMID
    Gene: PYRI4
    Organism Scientific: STREPTOMYCES RUGOSPORUS
    Organism Taxid: 295838

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
14W94Ligand/Ion(4S,4AS,6AS,8R,9R,10AR,13R,14AS,18AR,18BR)-9-ETHYL-4,8,19-TRIHYDROXY-10A,12,13,18A-TETRAMETHYL-2,3,4,4A,5,6,6A,7,8,9,10,10A,13,14,18A,18B-HEXADECAHYDRO-1H-14A,17-(METHENO)BENZO[B]NAPHTHO[2,1-H]AZACYCLODODECINE-16,18(15H,17H)-DIONE
2GOL8Ligand/IonGLYCEROL
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
14W92Ligand/Ion(4S,4AS,6AS,8R,9R,10AR,13R,14AS,18AR,18BR)-9-ETHYL-4,8,19-TRIHYDROXY-10A,12,13,18A-TETRAMETHYL-2,3,4,4A,5,6,6A,7,8,9,10,10A,13,14,18A,18B-HEXADECAHYDRO-1H-14A,17-(METHENO)BENZO[B]NAPHTHO[2,1-H]AZACYCLODODECINE-16,18(15H,17H)-DIONE
2GOL2Ligand/IonGLYCEROL
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
14W92Ligand/Ion(4S,4AS,6AS,8R,9R,10AR,13R,14AS,18AR,18BR)-9-ETHYL-4,8,19-TRIHYDROXY-10A,12,13,18A-TETRAMETHYL-2,3,4,4A,5,6,6A,7,8,9,10,10A,13,14,18A,18B-HEXADECAHYDRO-1H-14A,17-(METHENO)BENZO[B]NAPHTHO[2,1-H]AZACYCLODODECINE-16,18(15H,17H)-DIONE
2GOL6Ligand/IonGLYCEROL

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:65 , TYR A:85 , GLU A:87 , TYR A:89 , SER A:119 , MET A:163binding site for residue GOL A 201
02AC2SOFTWAREVAL A:131 , ARG A:148 , HOH A:302 , HOH A:306 , HOH A:322 , ARG B:148 , PHE B:162binding site for residue GOL A 202
03AC3SOFTWAREALA A:10 , GLU A:65 , LEU A:70 , GLU A:87 , GLN A:115 , HIS A:117 , CYS A:136 , MET A:139 , TYR A:177 , HOH A:347 , HOH A:368 , HOH A:380binding site for residue 4W9 A 203
04AC4SOFTWAREARG B:9 , ALA B:10 , GLU B:65 , LEU B:70 , GLU B:87 , GLN B:115 , HIS B:117 , CYS B:136 , MET B:139 , TYR B:177 , HOH B:329 , HOH B:391binding site for residue 4W9 B 201
05AC5SOFTWAREGLY A:77 , GLU C:129 , ARG C:152binding site for residue GOL C 201
06AC6SOFTWAREGLU C:65 , TYR C:85 , GLU C:87 , TYR C:89 , SER C:119 , MET C:163binding site for residue GOL C 202
07AC7SOFTWAREMET C:113 , THR C:137 , LEU C:140 , 4W9 C:205 , HOH C:307 , HOH C:317 , HOH C:355 , HOH C:405binding site for residue GOL C 203
08AC8SOFTWAREASP C:61 , HOH C:318binding site for residue GOL C 204
09AC9SOFTWAREALA C:10 , GLU C:65 , LEU C:70 , GLU C:87 , GLN C:115 , HIS C:117 , CYS C:136 , TYR C:177 , GOL C:203 , HOH C:307 , HOH C:312 , HOH C:400binding site for residue 4W9 C 205
10AD1SOFTWAREGLU D:65 , TYR D:85 , GLU D:87 , TYR D:89 , SER D:119 , MET D:163binding site for residue GOL D 201
11AD2SOFTWARETHR B:21 , GLU D:20 , THR D:21 , ILE D:22 , ARG D:141 , HOH D:313binding site for residue GOL D 202
12AD3SOFTWAREALA D:10 , GLU D:65 , LEU D:70 , GLU D:87 , GLN D:115 , HIS D:117 , ILE D:134 , CYS D:136 , MET D:139 , TYR D:177 , HOH D:317 , HOH D:341 , HOH D:348 , HOH D:383 , HOH D:414 , HOH D:417binding site for residue 4W9 D 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5BU3)

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Glu A:110 -Pro A:111
2Arg A:173 -Pro A:174
3Glu B:110 -Pro B:111
4Arg B:173 -Pro B:174
5Ala C:46 -Ala C:47
6Glu C:110 -Pro C:111
7Arg C:173 -Pro C:174
8Glu D:110 -Pro D:111
9Arg D:173 -Pro D:174

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5BU3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5BU3)

(-) Exons   (0, 0)

(no "Exon" information available for 5BU3)

(-) 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:181
                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.........hhhhhhhhhhhhh.......hhhhhhhhheeeeeeeeeeeeeeee........eeeeeeeee.....eeeeeeeeeeeee.....eeeeeeeeee..eeeeeeeeeehhhhhh...eeeeeeeeee.....eeeeeeeeee......eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bu3 A   4 PQIDERAMEAGAAALQETIVDPGPLDVTALAVAAALAAGLHSAADDPAAALDKCIVLDELTEFAEKLVVHDRPGGIGTTVEYVEVYEDASGVRLGTATGNAVVLKMEPHMWQFHQSVSELADGSFEAVGVIDCTAMLRRMTQVLRVTGRSGRYAGKSGFMTLAISDPNQRPPHYSVQVVLC 184
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183 


Chain B from PDB  Type:PROTEIN  Length:181
                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.........hhhhhhhhhhhhh.......hhhhhhhhheeeeeeeeeeeeeeee........eeeeeeeee.....eeeeeeeeeeeee.....eeeeeeeeee..eeeeeeeeeehhhhhh...eeeeeeeeee.....eeeeeeeeee......eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bu3 B   4 PQIDERAMEAGAAALQETIVDPGPLDVTALAVAAALAAGLHSAADDPAAALDKCIVLDELTEFAEKLVVHDRPGGIGTTVEYVEVYEDASGVRLGTATGNAVVLKMEPHMWQFHQSVSELADGSFEAVGVIDCTAMLRRMTQVLRVTGRSGRYAGKSGFMTLAISDPNQRPPHYSVQVVLC 184
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183 


Chain C from PDB  Type:PROTEIN  Length:181
                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.........hhhhhhhhhhhhhh........hhhhhh.eeeeeeeeeeeeeeee........eeeeeeeee.....eeeeeeeeeeeee.....eeeeeeeeee..eeeeeeeeeehhhhhh...eeeeeeeeee.....eeeeeeeeee......eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bu3 C   4 PQIDERAMEAGAAALQETIVDPGPLDVTALAVAAALAAGLHSAADDPAAALDKCIVLDELTEFAEKLVVHDRPGGIGTTVEYVEVYEDASGVRLGTATGNAVVLKMEPHMWQFHQSVSELADGSFEAVGVIDCTAMLRRMTQVLRVTGRSGRYAGKSGFMTLAISDPNQRPPHYSVQVVLC 184
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183 


Chain D from PDB  Type:PROTEIN  Length:181
                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.........hhhhhhhhhhhhh.......hhhhhhhh.eeeeeeeeeeeeeeee........eeeeeeeee.....eeeeeeeeeeeee.....eeeeeeeeee..eeeeeeeeeehhhhhh...eeeeeeeeee.....eeeeeeeeee......eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bu3 D   4 PQIDERAMEAGAAALQETIVDPGPLDVTALAVAAALAAGLHSAADDPAAALDKCIVLDELTEFAEKLVVHDRPGGIGTTVEYVEVYEDASGVRLGTATGNAVVLKMEPHMWQFHQSVSELADGSFEAVGVIDCTAMLRRMTQVLRVTGRSGRYAGKSGFMTLAISDPNQRPPHYSVQVVLC 184
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183
   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 5BU3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5BU3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5BU3)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5BU3)

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 Related Entries

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        K7QVW7_9ACTN | K7QVW7: 5btu

(-) Related Entries Specified in the PDB File

5btu