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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF E. COLI YDII COMPLEXED WITH 2,4-DIHYDROXYPHENACYL COA
 
Authors :  W. Ru, J. D. Farelli, D. Dunaway-Mariano, K. N. Allen
Date :  12 Apr 13  (Deposition) - 30 Jul 14  (Release) - 20 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  B,C  (1x)
Biol. Unit 2:  A,D  (1x)
Keywords :  Hot-Dog Fold, Thioesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Wu, J. A. Latham, D. Chen, J. Farelli, H. Zhao, K. Matthews, K. N. Allen, D. Dunaway-Mariano
Structure And Catalysis In The Escherichia Coli Hotdog-Fold Thioesterase Paralogs Ydii And Ybdb.
Biochemistry V. 53 4788 2014
PubMed-ID: 25010423  |  Reference-DOI: 10.1021/BI500334V

(-) Compounds

Molecule 1 - ESTERASE YDII
    Chains: C, B, D, A
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-23A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: B1686, JW1676, YDII
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):  BC 
Biological Unit 2 (1x): A  D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1HFQ4Ligand/Ion2,4-DIHYDROXYPHENACYL COENZYME A
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1HFQ2Ligand/Ion2,4-DIHYDROXYPHENACYL COENZYME A
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1HFQ2Ligand/Ion2,4-DIHYDROXYPHENACYL COENZYME A

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:109 , ARG A:110 , HOH A:354 , GLU B:63 , SER B:67 , VAL B:68 , LYS B:79 , VAL B:80 , GLY B:82 , LEU B:136 , HOH B:342 , GLN C:48 , PRO C:49 , LEU C:53 , HIS C:54 , GLY C:55 , HIS C:89 , VAL C:90 , ARG C:91 , SER C:92 , ARG C:110 , HOH C:310 , HOH C:315 , HOH C:324 , HOH C:349 , HOH C:359 , HOH C:386 , HOH C:423 , HIS D:106 , GLY D:108 , SER D:109 , ARG D:110 , HIS D:111BINDING SITE FOR RESIDUE HFQ C 201
2AC2SOFTWAREHIS A:106 , GLY A:108 , SER A:109 , ARG A:110 , HIS A:111 , HOH A:301 , GLN B:48 , PRO B:49 , LEU B:53 , HIS B:54 , GLY B:55 , HIS B:89 , VAL B:90 , ARG B:91 , SER B:92 , HOH B:303 , HOH B:309 , HOH B:311 , HOH B:324 , HOH B:347 , HOH B:349 , HOH B:361 , HOH B:380 , HOH B:431 , HOH B:451 , HOH B:481 , GLU C:63 , SER C:67 , VAL C:80 , GLY C:82 , LYS D:4 , SER D:109BINDING SITE FOR RESIDUE HFQ B 201
3AC3SOFTWAREGLU A:63 , SER A:67 , GLY A:82 , LEU A:136 , GLU B:77 , LYS B:79 , HIS C:106 , GLY C:108 , SER C:109 , ARG C:110 , HIS C:111 , GLN D:48 , PRO D:49 , LEU D:53 , HIS D:54 , GLY D:55 , HIS D:89 , VAL D:90 , ARG D:91 , SER D:92 , ARG D:94 , HOH D:313 , HOH D:316 , HOH D:333 , HOH D:352 , HOH D:353 , HOH D:398 , HOH D:402 , HOH D:408 , HOH D:428 , HOH D:448BINDING SITE FOR RESIDUE HFQ D 201
4AC4SOFTWAREGLN A:48 , PRO A:49 , LEU A:53 , HIS A:54 , GLY A:55 , HIS A:89 , VAL A:90 , ARG A:91 , SER A:92 , HOH A:304 , HOH A:310 , HOH A:311 , HOH A:319 , HOH A:359 , HOH A:361 , HOH A:376 , HOH A:378 , HOH A:382 , HIS B:106 , GLY B:108 , SER B:109 , ARG B:110 , HIS B:111 , HOH B:462 , GLU C:77 , GLU D:63 , SER D:67 , VAL D:68 , VAL D:80 , GLY D:82 , LEU D:136BINDING SITE FOR RESIDUE HFQ A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K49)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4K49)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K49)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K49)

(-) Exons   (0, 0)

(no "Exon" information available for 4K49)

(-) 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:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhh...hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhh......eeeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k49 A   1 MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL 136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      


Chain B from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhh...hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k49 B   1 MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL 136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      


Chain C from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhh...hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhhh......eeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k49 C   1 MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL 136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      


Chain D from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhh...hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhh......eeeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k49 D   1 MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL 136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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 4K49)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K49)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K49)

(-) Gene Ontology  (5, 5)

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 Related Entries

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

UniProtKB/Swiss-Prot
        MENI_ECOLI | P77781: 1sbk 1vh5 1vi8 4k4a 4k4b

(-) Related Entries Specified in the PDB File

1sbk ECOLI YDII APO STRUCTURE
4k4a
4k4b
4k4c
4k4d