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(-) Description

Title :  DIHYDRODIPICOLINATE SYNTHASE FROM C. JEJUNI WITH PYRUVATE BOUND TO THE ACTIVE SITE
 
Authors :  C. J. T. Conly
Date :  30 Jul 13  (Deposition) - 14 Jan 15  (Release) - 14 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Schiff-Base, Aldolase, Tim Barrel, Type 1 Aldolase Catalysing Condensation Of Pyruvate And S-Aspartate-B-Semi-Aldehyde, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. J. Conly, Y. V. Skovpen, S. Li, D. R. Palmer, D. A. Sanders
Tyrosine 110 Plays A Critical Role In Regulating The Allosteric Inhibition Of Campylobacter Jejuni Dihydrodipicolinate Synthase By Lysine.
Biochemistry V. 53 7396 2014
PubMed-ID: 25369463  |  Reference-DOI: 10.1021/BI5012157

(-) 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: CJ0806, DAPA
    Organism Scientific: CAMPYLOBACTER JEJUNI SUBSP. JEJUNI
    Organism Taxid: 192222
    Strain: NCTC 11168
    Synonym: HTPA SYNTHASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 46)

Asymmetric/Biological Unit (6, 46)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2EDO21Ligand/Ion1,2-ETHANEDIOL
3GOL5Ligand/IonGLYCEROL
4KPI4Mod. Amino Acid(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC ACID
5PG42Ligand/IonTETRAETHYLENE GLYCOL
6PGE11Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (39, 39)

Asymmetric Unit (39, 39)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:223 , PHE A:224BINDING SITE FOR RESIDUE EDO A 301
02AC2SOFTWAREGLY A:20 , ARG A:272 , PGE A:304BINDING SITE FOR RESIDUE PGE A 302
03AC3SOFTWAREALA A:127 , GLN A:128 , VAL A:130 , ASP A:131 , ASN A:161BINDING SITE FOR RESIDUE EDO A 303
04AC4SOFTWAREPHE A:271 , ARG A:272 , LEU A:273 , PGE A:302 , HOH A:434BINDING SITE FOR RESIDUE PGE A 304
05AC5SOFTWAREMET A:186 , LYS A:204BINDING SITE FOR RESIDUE PGE A 305
06AC6SOFTWAREASP A:238 , GLU A:239 , TYR A:241 , ASN A:242 , HIS B:181BINDING SITE FOR RESIDUE EDO A 306
07AC7SOFTWAREALA A:263 , GLY A:264 , ILE A:295 , GLY A:297 , HOH A:523BINDING SITE FOR RESIDUE PGE A 307
08AC8SOFTWAREGLU A:36 , EDO D:303BINDING SITE FOR RESIDUE ACT A 308
09AC9SOFTWARESER A:200 , GLY A:202 , TYR A:230 , LYS B:234BINDING SITE FOR RESIDUE EDO A 309
10BC1SOFTWARETHR A:149 , ASP A:150 , ASP A:177 , HIS A:181 , ACT A:312BINDING SITE FOR RESIDUE GOL A 310
11BC2SOFTWAREPRO A:278BINDING SITE FOR RESIDUE EDO A 311
12BC3SOFTWAREARG A:157 , GOL A:310BINDING SITE FOR RESIDUE ACT A 312
13BC4SOFTWAREGLN A:117 , TYR A:120 , ASP A:150 , LYS A:154BINDING SITE FOR RESIDUE PG4 A 313
14BC5SOFTWARESER A:51 , LEU A:54 , HIS A:56 , HIS A:59 , HOH A:444 , HOH A:488BINDING SITE FOR RESIDUE GOL A 314
15BC6SOFTWAREGLN B:117 , ASP B:150 , THR B:151 , LYS B:154BINDING SITE FOR RESIDUE PGE B 301
16BC7SOFTWAREARG B:142 , KPI B:166 , PHE B:248 , ASN B:252 , HOH B:472BINDING SITE FOR RESIDUE GOL B 302
17BC8SOFTWAREMET B:186 , LYS B:204 , LEU B:226 , LYS C:231BINDING SITE FOR RESIDUE PGE B 303
18BC9SOFTWAREILE B:7 , LEU B:226BINDING SITE FOR RESIDUE EDO B 304
19CC1SOFTWARETYR B:261 , LEU B:262BINDING SITE FOR RESIDUE PGE B 305
20CC2SOFTWAREHIS B:223 , PHE B:224 , ASP B:227 , HOH D:496BINDING SITE FOR RESIDUE PGE B 306
21CC3SOFTWARESER B:51 , LEU B:54 , HIS B:56 , HIS B:59BINDING SITE FOR RESIDUE GOL B 307
22CC4SOFTWAREASP B:150 , ASP B:177 , HIS B:181BINDING SITE FOR RESIDUE EDO B 308
23CC5SOFTWAREARG B:29 , ARG B:33 , PHE B:298BINDING SITE FOR RESIDUE EDO B 309
24CC6SOFTWAREGLN C:117 , TYR C:120 , THR C:151 , LYS C:154 , HOH C:511 , HOH C:527BINDING SITE FOR RESIDUE PG4 C 301
25CC7SOFTWAREVAL C:90 , LYS C:94BINDING SITE FOR RESIDUE EDO C 302
26CC8SOFTWAREGLY C:91 , LEU C:92BINDING SITE FOR RESIDUE EDO C 303
27CC9SOFTWAREILE C:7 , MET C:186 , LYS C:204 , LEU C:226BINDING SITE FOR RESIDUE PGE C 304
28DC1SOFTWAREALA C:263 , GLY C:297BINDING SITE FOR RESIDUE EDO C 305
29DC2SOFTWAREPHE C:224BINDING SITE FOR RESIDUE EDO C 306
30DC3SOFTWAREASP C:150 , ASP C:177 , HIS C:181BINDING SITE FOR RESIDUE EDO C 307
31DC4SOFTWAREPRO C:140 , GLY C:141 , SER C:169 , HOH C:466BINDING SITE FOR RESIDUE PGE C 308
32DC5SOFTWAREARG C:142 , PHE C:248 , SER C:251 , ASN C:252BINDING SITE FOR RESIDUE ACT C 309
33DC6SOFTWAREGLN D:117 , TYR D:120 , ASP D:150 , THR D:151 , LYS D:154BINDING SITE FOR RESIDUE PGE D 301
34DC7SOFTWARELEU D:54 , HIS D:56 , HIS D:59 , HOH D:494 , HOH D:538BINDING SITE FOR RESIDUE GOL D 302
35DC8SOFTWAREACT A:308 , TYR D:261BINDING SITE FOR RESIDUE EDO D 303
36DC9SOFTWARELYS C:234 , SER D:200 , GLY D:202 , TYR D:230BINDING SITE FOR RESIDUE EDO D 304
37EC1SOFTWAREHOH B:467 , HOH D:438BINDING SITE FOR RESIDUE EDO D 307
38EC2SOFTWAREHIS D:223BINDING SITE FOR RESIDUE EDO D 308
39EC3SOFTWAREASP D:2 , LYS D:3 , PHE D:156 , ARG D:184BINDING SITE FOR RESIDUE EDO D 309

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LY8)

(-) 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 4LY8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LY8)

(-) Exons   (0, 0)

(no "Exon" information available for 4LY8)

(-) 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:298
                                                                                                                                                                                                                                                                                                                                          
               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
                 4ly8 A   1 MDKNIIIGAMTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGADGILSVAPYYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVkEASGNIDKCVDLLAHEPRMMLISGEDAINYPILSNGGKGVISVTSNLLPDMISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAMYLAGLIESLEFRLPLCSPSKENFAKIEEVMKKYKIKGF 298
                                    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       270       280       290        
                                                                                                                                                                                               166-KPI                                                                                                                                


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
                 4ly8 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-KPI                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:298
                                                                                                                                                                                                                                                                                                                                          
               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
                 4ly8 C   1 MDKNIIIGAMTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGADGILSVAPYYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVkEASGNIDKCVDLLAHEPRMMLISGEDAINYPILSNGGKGVISVTSNLLPDMISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAMYLAGLIESLEFRLPLCSPSKENFAKIEEVMKKYKIKGF 298
                                    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       270       280       290        
                                                                                                                                                                                               166-KPI                                                                                                                                


Chain D 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..hhhhhhhhhhhhhhhhhhhhhhhhhh....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
                 4ly8 D   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-KPI
   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 4LY8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LY8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LY8)

(-) 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 4m19 4mlj 4mlr 4r53 5f1u 5f1v

(-) Related Entries Specified in the PDB File

4m19