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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 :  2.20
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, 21)

Asymmetric/Biological Unit (5, 21)
No.NameCountTypeFull Name
13VN4Ligand/Ion(2R,5R)-2,5-DIAMINO-2,5-BIS(4-AMINOBUTYL)HEXANEDIOICACID
2EDO9Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL
4MCL4Mod. Amino AcidNZ-(1-CARBOXYETHYLIDENE)-LYSINE
5PGE3Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:67 , CYS A:70 , LYS A:71 , THR A:73 , LYS A:74 , LYS A:76 , GLY A:100 , ASP A:102 , HOH A:437 , HOH A:444 , ASP B:227 , LYS B:231 , GLU B:232binding site for residue 3VN A 301
02AC2SOFTWAREGLN A:117 , TYR A:120 , ASP A:150 , THR A:151 , LYS A:154 , GLU D:267binding site for residue PGE A 302
03AC3SOFTWARELYS A:204binding site for residue EDO A 303
04AC4SOFTWARESER A:51 , ALA A:52 , LEU A:54 , HIS A:56 , HIS A:59 , ASN A:84 , GLU A:88 , TYR A:110 , HOH A:430 , HOH A:433 , HOH A:445 , SER C:51 , ALA C:52 , LEU C:54 , HIS C:59 , ASN C:84 , GLU C:88 , TYR C:110binding site for residue 3VN A 304
05AC5SOFTWAREGLN B:117 , TYR B:120 , THR B:151 , LYS B:154 , HOH B:457binding site for residue PGE B 301
06AC6SOFTWAREALA B:263 , ILE B:295 , GLY B:297binding site for residue EDO B 302
07AC7SOFTWAREHIS B:223 , PHE B:224binding site for residue EDO B 303
08AC8SOFTWARELYS B:94binding site for residue EDO B 304
09AC9SOFTWARESER B:51 , ALA B:52 , LEU B:54 , HIS B:56 , HIS B:59 , ASN B:84 , GLU B:88 , TYR B:110 , HOH B:411 , HOH B:421 , HOH B:469 , SER D:51 , ALA D:52 , LEU D:54 , HIS D:59 , ASN D:84 , GLU D:88 , TYR D:110 , HOH D:466binding site for residue 3VN B 305
10AD1SOFTWARETYR B:261 , HOH B:427 , LYS C:292binding site for residue EDO C 301
11AD2SOFTWAREALA C:263 , ILE C:295 , GLY C:297binding site for residue EDO C 302
12AD3SOFTWARELEU A:273 , THR C:86 , HIS C:87binding site for residue GOL C 303
13AD4SOFTWAREGLN D:117 , TYR D:120 , ASP D:150 , THR D:151 , LYS D:154binding site for residue PGE D 301
14AD5SOFTWAREGLU D:146 , SER D:148 , THR D:149 , LYS D:174 , HOH D:403binding site for residue EDO D 302
15AD6SOFTWARELYS D:32 , THR D:69binding site for residue EDO D 303
16AD7SOFTWAREHIS D:223binding site for residue EDO D 304
17AD8SOFTWARECYS D:70 , LYS D:71 , THR D:73 , LYS D:76 , GLY D:100 , ALA D:101 , ASP D:102 , ILE D:132 , HOH D:401binding site for residue 3VN D 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F1V)

(-) 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 5F1V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F1V)

(-) Exons   (0, 0)

(no "Exon" information available for 5F1V)

(-) 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:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....ee..eehhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f1v A   3 KNIIIGAMTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGADGILSVAPYYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVkEASGNIDKCVDLLAHEPRMMLISGEDAINYPILSNGGKGVISVTSNLLPDMISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAMYLAGLIESLEFRLPLCSPSKENFAKIEEVMKKYKIKGF 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      
                                                                                                                                                                                             166-MCL                                                                                                                                


Chain B 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......hhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f1v B   2 DKNIIIGAMTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGADGILSVAPYYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVkEASGNIDKCVDLLAHEPRMMLISGEDAINYPILSNGGKGVISVTSNLLPDMISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAMYLAGLIESLEFRLPLCSPSKENFAKIEEVMKKYKIKGF 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       
                                                                                                                                                                                              166-MCL                                                                                                                                


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......hhhhhhhhhhhhhhhhhhhhhh....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
                 5f1v C   3 KNIIIGAMTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGADGILSVAPYYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVkEASGNIDKCVDLLAHEPRMMLISGEDAINYPILSNGGKGVISVTSNLLPDMISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAMYLAGLIESLEFRLPLCSPSKENFAKIEEVMKKYKIKGF 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      
                                                                                                                                                                                             166-MCL                                                                                                                                


Chain D from PDB  Type:PROTEIN  Length:295
                                                                                                                                                                                                                                                                                                                                       
               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
                 5f1v D   4 NIIIGAMTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGADGILSVAPYYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVkEASGNIDKCVDLLAHEPRMMLISGEDAINYPILSNGGKGVISVTSNLLPDMISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAMYLAGLIESLEFRLPLCSPSKENFAKIEEVMKKYKIKGF 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     
                                                                                                                                                                                            166-MCL
   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 5F1V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F1V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F1V)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DAPA_CAMJE | Q9PPB4: 3ler 3m5v 4ly8 4m19 4mlj 4mlr 4r53 5f1u

(-) Related Entries Specified in the PDB File

5f1u