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(-) Description

Title :  BIOMIMETIC DESIGN RESULTS IN A POTENT ALLOSTERIC INHIBITOR OF DIHYDRODIPICOLINATE SYNTHASE FROM CAMPYLOBACTER JEJUNI
 
Authors :  C. J. T. Conly, D. R. J. Palmer, D. A. R. Sanders
Date :  30 Nov 15  (Deposition) - 17 Feb 16  (Release) - 24 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Schiff-Base, Aldolase, Tim Barrel, Lyase-Lyase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. V. Skovpen, C. J. Conly, D. A. Sanders, D. R. Palmer
Biomimetic Design Results In A Potent Allosteric Inhibitor Of Dihydrodipicolinate Synthase From Campylobacter Jejuni.
J. Am. Chem. Soc. V. 138 2014 2016
PubMed-ID: 26836694  |  Reference-DOI: 10.1021/JACS.5B12695

(-) Compounds

Molecule 1 - 4-HYDROXY-TETRAHYDRODIPICOLINATE SYNTHASE
    Chains: A, B, C, D
    EC Number: 4.3.3.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-80L
    Expression System Strain: XL1-BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DAPA
    Organism Scientific: CAMPYLOBACTER JEJUNI
    Organism Taxid: 197
    Synonym: HTPA SYNTHASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric/Biological Unit (5, 15)
No.NameCountTypeFull Name
13VN2Ligand/Ion(2R,5R)-2,5-DIAMINO-2,5-BIS(4-AMINOBUTYL)HEXANEDIOICACID
2CL1Ligand/IonCHLORIDE ION
3EDO10Ligand/Ion1,2-ETHANEDIOL
4PG41Ligand/IonTETRAETHYLENE GLYCOL
5PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:51 , ALA A:52 , LEU A:54 , HIS A:59 , ASN A:84 , GLU A:88 , PHE A:110 , HOH A:441 , SER B:51 , ALA B:52 , LEU B:54 , HIS B:56 , HIS B:59 , ASN B:84 , GLU B:88 , PHE B:110 , EDO B:305 , HOH B:403 , HOH B:434binding site for residue 3VN A 301
02AC2SOFTWAREGLN A:117 , TYR A:120 , ASP A:150 , THR A:151 , LYS A:154binding site for residue PG4 A 302
03AC3SOFTWAREALA A:263 , GLY A:264 , GLY A:297binding site for residue EDO A 303
04AC4SOFTWAREGLY A:144binding site for residue EDO A 304
05AC5SOFTWARETHR A:69 , LYS A:71 , THR A:73binding site for residue EDO A 305
06AC6SOFTWAREGLY B:46 , THR B:47 , THR B:48 , LYS B:166binding site for residue CL B 301
07AC7SOFTWAREGLN B:117 , TYR B:120 , THR B:151 , LYS B:154binding site for residue PGE B 302
08AC8SOFTWARELYS B:32 , THR B:69binding site for residue EDO B 304
09AC9SOFTWAREALA A:52 , LEU A:54 , THR A:55 , 3VN A:301 , HIS B:87 , GLU B:88 , HOH B:419 , HOH B:441binding site for residue EDO B 305
10AD1SOFTWARECYS C:70 , GLY C:72 , THR C:73 , VAL C:75 , ASP C:102binding site for residue EDO C 301
11AD2SOFTWARETYR C:261binding site for residue EDO C 302
12AD3SOFTWARESER C:51 , ALA C:52 , LEU C:54 , HIS C:59 , ASN C:84 , GLU C:88 , SER D:51 , ALA D:52 , LEU D:54 , HIS D:59 , ASN D:84 , GLU D:88 , PHE D:110 , HOH D:405 , HOH D:423binding site for residue 3VN D 301
13AD4SOFTWARETYR D:261 , LEU D:262binding site for residue EDO D 302
14AD5SOFTWAREASP D:150 , THR D:151 , LYS D:154binding site for residue EDO D 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F1U)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Asn A:252 -Pro A:253
2Leu A:273 -Pro A:274
3Asn B:252 -Pro B:253
4Leu B:273 -Pro B:274
5Asn C:252 -Pro C:253
6Leu C:273 -Pro C:274
7Asn D:252 -Pro D:253
8Leu D:273 -Pro D:274

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F1U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F1U)

(-) Exons   (0, 0)

(no "Exon" information available for 5F1U)

(-) 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:297
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee....ee..eehhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhh.....eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f1u A   2 DKNIIIGAMTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGADGILSVAPFYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVKEASGNIDKCVDLLAHEPRMMLISGEDAINYPILSNGGKGVISVTSNLLPDMISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAMYLAGLIESLEFRLPLCSPSKENFAKIEEVMKKYKIKGF 298
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       


Chain B from PDB  Type:PROTEIN  Length:295
                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....ee..eehhhhhhhhhhhhhh....eee...........hhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhh.....eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f1u B   4 NIIIGAMTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGADGILSVAPFYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVKEASGNIDKCVDLLAHEPRMMLISGEDAINYPILSNGGKGVISVTSNLLPDMISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAMYLAGLIESLEFRLPLCSPSKENFAKIEEVMKKYKIKGF 298
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293     


Chain C from PDB  Type:PROTEIN  Length:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....ee..eehhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhh.....eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f1u C   3 KNIIIGAMTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGADGILSVAPFYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVKEASGNIDKCVDLLAHEPRMMLISGEDAINYPILSNGGKGVISVTSNLLPDMISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAMYLAGLIESLEFRLPLCSPSKENFAKIEEVMKKYKIKGF 298
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292      


Chain D from PDB  Type:PROTEIN  Length:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....ee..eehhhhhhhhhhhhhh....eee...........hhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f1u D   3 KNIIIGAMTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGADGILSVAPFYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVKEASGNIDKCVDLLAHEPRMMLISGEDAINYPILSNGGKGVISVTSNLLPDMISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAMYLAGLIESLEFRLPLCSPSKENFAKIEEVMKKYKIKGF 298
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292
   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 5F1U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F1U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F1U)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        DAPA_CAMJE | Q9PPB4: 3ler 3m5v 4ly8 4m19 4mlj 4mlr 4r53 5f1v

(-) Related Entries Specified in the PDB File

5f1v