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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF E. COLI YBDB COMPLEXED WITH PHENACYL-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 :  1.85
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Hotdog 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 - PROOFREADING THIOESTERASE ENTH
    Chains: A, B, C, D
    EC Number: 3.1.2.-
    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: B0597, ENTH, JW0589, YBDB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
    Synonym: ENTEROBACTIN SYNTHASE COMPONENT H, P15

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
10FQ4Ligand/IonPHENACYL COENZYME A
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
10FQ2Ligand/IonPHENACYL COENZYME A
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
10FQ2Ligand/IonPHENACYL COENZYME A

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:48 , PRO A:49 , LEU A:53 , HIS A:54 , GLY A:55 , ASP A:76 , GLY A:77 , HIS A:89 , HIS A:90 , ARG A:91 , PRO A:92 , HOH A:303 , HOH A:393 , HIS B:106 , GLY B:108 , ARG B:109 , GLN B:110 , ASN B:111 , GLU D:63 , SER D:67 , MET D:68 , GLY D:82 , THR D:83BINDING SITE FOR RESIDUE 0FQ A 201
2AC2SOFTWAREHIS A:106 , GLY A:108 , ARG A:109 , GLN A:110 , ASN A:111 , GLN B:48 , PRO B:49 , PHE B:50 , LEU B:53 , HIS B:54 , GLY B:55 , GLY B:77 , HIS B:89 , HIS B:90 , ARG B:91 , PRO B:92 , HOH B:304 , GLU C:63 , SER C:67 , MET C:68 , VAL C:81 , GLY C:82BINDING SITE FOR RESIDUE 0FQ B 201
3AC3SOFTWAREGLU B:63 , SER B:67 , MET B:68 , VAL B:81 , GLY B:82 , THR B:83 , GLN C:48 , PRO C:49 , LEU C:53 , HIS C:54 , GLY C:55 , HIS C:89 , HIS C:90 , ARG C:91 , PRO C:92 , HOH C:306 , HOH C:358 , GLY D:108 , ARG D:109 , GLN D:110 , ASN D:111BINDING SITE FOR RESIDUE 0FQ C 201
4AC4SOFTWAREGLU A:63 , SER A:67 , MET A:68 , GLY A:82 , THR A:83 , LEU A:136 , HIS C:106 , GLY C:108 , ARG C:109 , GLN C:110 , ASN C:111 , GLN D:48 , PRO D:49 , LEU D:53 , HIS D:54 , GLY D:55 , ARG D:75 , HIS D:89 , HIS D:90 , ARG D:91 , PRO D:92 , HOH D:313BINDING SITE FOR RESIDUE 0FQ D 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K4C)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu B:136 -Gly B:137

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K4C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K4C)

(-) Exons   (0, 0)

(no "Exon" information available for 4K4C)

(-) 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:137
                                                                                                                                                                         
               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
                 4k4c A   1 MIWKRHLTLDELNATSDNTMVAHLGIVYTRLGDDVLEAEMPVDTRTHQPFGLLHGGASAALAETLGSMAGFMMTRDGQCVVGTELNATHHRPVSEGKVRGVCQPLHLGRQNQSWEIVVFDEQGRRCCTCRLGTAVLG 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       


Chain B from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh..hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k4c B   1 MIWKRHLTLDELNATSDNTMVAHLGIVYTRLGDDVLEAEMPVDTRTHQPFGLLHGGASAALAETLGSMAGFMMTRDGQCVVGTELNATHHRPVSEGKVRGVCQPLHLGRQNQSWEIVVFDEQGRRCCTCRLGTAVLG 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       


Chain C from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhh.hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhh......eeeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k4c C   1 MIWKRHLTLDELNATSDNTMVAHLGIVYTRLGDDVLEAEMPVDTRTHQPFGLLHGGASAALAETLGSMAGFMMTRDGQCVVGTELNATHHRPVSEGKVRGVCQPLHLGRQNQSWEIVVFDEQGRRCCTCRLGTAVLG 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       


Chain D from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                         
               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
                 4k4c D   1 MIWKRHLTLDELNATSDNTMVAHLGIVYTRLGDDVLEAEMPVDTRTHQPFGLLHGGASAALAETLGSMAGFMMTRDGQCVVGTELNATHHRPVSEGKVRGVCQPLHLGRQNQSWEIVVFDEQGRRCCTCRLGTAVLG 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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 4K4C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K4C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K4C)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        ENTH_ECOLI | P0A8Y8: 1vh9 4k4d

(-) Related Entries Specified in the PDB File

1vh9 4k49 4k4a 4k4b 4k4d