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(-) Description

Title :  STREPTOMYCES BINGCHENGGENSIS ALDOLASE-DEHYDRATASE IN SCHIFF BASE COMPLEX WITH PYRUVATE
 
Authors :  L. S. Mueller, N. R. Silvaggi
Date :  15 Apr 15  (Deposition) - 17 Jun 15  (Release) - 15 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Aldolase, Dehydratase, Acetoacetate Decarboxylase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. S. Mueller, R. W. Hoppe, J. M. Ochsenwald, R. T. Berndt, G. B. Severin A. W. Schwabacher, N. R. Silvaggi
Sbi00515, A Protein Of Unknown Function From Streptomyces Bingchenggensis, Highlights The Functional Versatility Of The Acetoacetate Decarboxylase Scaffold.
Biochemistry V. 54 3978 2015
PubMed-ID: 26039798  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B00483

(-) Compounds

Molecule 1 - ACETOACETATE DECARBOXYLASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PE-SUMOKAN
    Expression System Strain: BL21STAR(DE3)
    Expression System Taxid: 469008
    Gene: SBI_00515
    Organism Scientific: STREPTOMYCES BINGCHENGGENSIS (STRAIN BCW-1)
    Organism Taxid: 749414
    Strain: BCW-1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric/Biological Unit (4, 14)
No.NameCountTypeFull Name
1FMT6Ligand/IonFORMIC ACID
2PE42Ligand/Ion2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
4PYR4Ligand/IonPYRUVIC ACID

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:24 , TYR A:82 , ALA A:111 , ARG A:114 , GLN A:118 , PHE A:120 , LYS A:122binding site for residue PYR A 301
02AC2SOFTWARELYS A:164 , ILE A:165 , THR A:166 , THR A:221 , ALA A:222 , ASP A:223 , HOH A:409binding site for residue FMT A 302
03AC3SOFTWAREGLY A:71 , GLU A:73 , LEU A:75 , ASP A:76 , ARG A:241 , THR D:152 , ALA D:163binding site for residue PE4 A 303
04AC4SOFTWARELYS B:164 , ILE B:165 , THR B:166 , THR B:221 , ALA B:222 , HOH B:444binding site for residue FMT B 302
05AC5SOFTWAREALA C:193 , GLY C:194 , GLN C:195 , HIS C:196 , HOH C:484binding site for residue FMT C 302
06AC6SOFTWARELYS C:164 , ILE C:165 , THR C:166 , THR C:221 , ALA C:222 , HOH C:418binding site for residue FMT C 303
07AC7SOFTWARELEU B:75 , ASP B:76 , ALA C:163 , HOH C:499 , HIS D:230binding site for residue PEG C 304
08AC8SOFTWAREHIS A:230 , HOH B:541 , GLY C:71 , GLU C:73 , LEU C:75 , ASP C:76 , ARG C:241 , HOH C:413 , HOH C:559binding site for residue PE4 C 305
09AC9SOFTWARETYR A:24 , ALA A:25 , ALA A:251 , TYR A:252 , GLY D:136 , GLY D:137 , PRO D:138 , GLY D:139 , HOH D:444binding site for residue FMT D 302
10AD1SOFTWAREHOH B:416 , ALA D:193 , GLY D:194 , GLN D:195 , HIS D:196binding site for residue FMT D 303
11AD2SOFTWARETHR A:152 , ALA A:163 , HIS B:230 , LEU D:75 , ASP D:76 , HOH D:600binding site for residue PEG D 304
12AD3SOFTWARETYR B:24 , TYR B:82 , GLU B:84 , ILE B:104 , VAL B:106 , ALA B:111 , MET B:112 , ARG B:114 , GLY B:115 , TRP B:116 , GLN B:118 , PHE B:120 , PRO B:121 , LYS B:123 , HOH B:505binding site for residue PYR B 301
13AD4SOFTWARELEU A:16 , TYR C:24 , TYR C:82 , ILE C:104 , ALA C:111 , MET C:112 , ARG C:114 , GLY C:115 , TRP C:116 , GLN C:118 , PHE C:120 , PRO C:121 , LYS C:123binding site for residue PYR C 301
14AD5SOFTWARELEU B:16 , TYR D:24 , TYR D:82 , GLU D:84 , ILE D:104 , ALA D:111 , MET D:112 , ARG D:114 , GLY D:115 , TRP D:116 , GLN D:118 , PHE D:120 , PRO D:121 , LYS D:123 , HOH D:476binding site for residue PYR D 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Val A:6 -Pro A:7
2Pro A:20 -Pro A:21
3Val B:6 -Pro B:7
4Pro B:20 -Pro B:21
5Val C:6 -Pro C:7
6Pro C:20 -Pro C:21
7Val D:6 -Pro D:7
8Pro D:20 -Pro D:21

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZBT)

(-) 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:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeeeeeeeee.hhhhhhhh.....ee......eeeeeeeeeeee...hhhhhhhhheeeeeeeeeeeee..eeeee...eee.hhhhhhhhhhhh..eee.eeee..................eeeeeeee..eeeeeeeeeeeee..hhhhh....eeeeeee............eeeeeee..eeeeeeeeeeeeeeeee......hhhhh...eeeeeeeeeeeeee..eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zbt A   1 MKGYTVPLSPRGIANLAPAPPWHYAGTVVGVEFFTDPAAAAATLPEGLTPDPDSAGRGVAMFIDWQYSSTGLEYLDPARSQYREFLITLDAHCNGAPVAWCPYIYVDNDAAMARGWVQGFPKKLGAVHQTRAYSVGGPGTPVLGPGGQFGATASSAGQRIAEAKITLEQPVPDPAALMSRPVINLRHFPRLAAGQHDQPAVHELVMSVLDDTAVSDAWVGTADLAFLPAHGEELADLPVRRTGKGFHFDLAYTVTDLMTL 260
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260


Chain B from PDB  Type:PROTEIN  Length:254
                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeeeeeeeee.hhhhhhhh.....ee......eeeeeeeeeeee...hhhhhhhhheeeeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhh..eee.eeee..................eeeeeeee..eeeeeeeeeeeee.....eeeeeee............eeeeeee..eeeeeeeeeeeeeeeee......hhhhh...eeeeeeeeeeeeee..eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zbt B   1 MKGYTVPLSPRGIANLAPAPPWHYAGTVVGVEFFTDPAAAAATLPEGLTPDPDSAGRGVAMFIDWQYSSTGLEYLDPARSQYREFLITLDAHCNGAPVAWCPYIYVDNDAAMARGWVQGFPKKLGAVHQTRAYSVGGPGTPVLGPGGQFGATASSAGQRIAEAKITLEQPVPSRPVINLRHFPRLAAGQHDQPAVHELVMSVLDDTAVSDAWVGTADLAFLPAHGEELADLPVRRTGKGFHFDLAYTVTDLMTL 260
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 ||    186       196       206       216       226       236       246       256    
                                                                                                                                                                                                     172|                                                                                 
                                                                                                                                                                                                      179                                                                                 


Chain C from PDB  Type:PROTEIN  Length:252
                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....................eeeeeeeeeeeee.hhhhhhhh.............eeeeeeeeeeee...hhhhhhhhheeeeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhh..eee.eeee..................eeeeeeee..eeeeeeeeeeeee...eeeeeee............eeeeeee..eeeeeeeeeeeeeeeee......hhhhh...eeeeeeeeeeeeee..eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4zbt C   1 MKGYTVPLSPRGIANLAPAPPWHYAGTVVGVEFFTDPAAAAATLPEGLTPDPDSAGRGVAMFIDWQYSSTGLEYLDPARSQYREFLITLDAHCNGAPVAWCPYIYVDNDAAMARGWVQGFPKKLGAVHQTRAYSVGGPGTPVLGPGGQFGATASSAGQRIAEAKITLEQPVRPVINLRHFPRLAAGQHDQPAVHELVMSVLDDTAVSDAWVGTADLAFLPAHGEELADLPVRRTGKGFHFDLAYTVTDLMTL 260
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170||     188       198       208       218       228       238       248       258  
                                                                                                                                                                                                    171|                                                                                
                                                                                                                                                                                                     180                                                                                


Chain D from PDB  Type:PROTEIN  Length:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeeeeeeeee.hhhhhhhh.....ee......eeeeeeeeeeee...hhhhhhhhheeeeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhh..eee.eeee..................eeeeeeee..eeeeeeeeeeeee..hhhhh....eeeeeee............eeeeee...eeeeeeeeeeeeeeeee......hhhhh...eeeeeeeeeeeeee...eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zbt D   1 MKGYTVPLSPRGIANLAPAPPWHYAGTVVGVEFFTDPAAAAATLPEGLTPDPDSAGRGVAMFIDWQYSSTGLEYLDPARSQYREFLITLDAHCNGAPVAWCPYIYVDNDAAMARGWVQGFPKKLGAVHQTRAYSVGGPGTPVLGPGGQFGATASSAGQRIAEAKITLEQPVPDPAALMSRPVINLRHFPRLAAGQHDQPAVHELVMSVLDDTAVSDAWVGTADLAFLPAHGEELADLPVRRTGKGFHFDLAYTVTDLMTLAD 262
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260
   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 4ZBT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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        D7C0E5_STRBB | D7C0E5: 4zbo

(-) Related Entries Specified in the PDB File

4zbo 4ZBO CONTAINS THE SAME PROTEIN WITH FORMATE BOUND.