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(-) Description

Title :  CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM CAMPYLOBACTER JEJUNI SUBSP. JEJUNI NCTC 11168
 
Authors :  Y. Kim, M. Zhou, J. Hasseman, W. F. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
Date :  15 Jan 10  (Deposition) - 26 Jan 10  (Release) - 26 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tim Barrel, Amino-Acid Biosynthesis, Cytoplasm, Diaminopimelate Biosynthesis, Lyase, Lysine Biosynthesis, Schiff Base, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, M. Zhou, J. Hasseman, W. F. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of Dihydrodipicolinate Synthase From Campylobacter Jejuni Subsp. Jejuni Nctc 11168
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIHYDRODIPICOLINATE SYNTHASE
    Chains: A, B, C, D
    EC Number: 4.2.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21 MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DAPA
    Organism Scientific: CAMPYLOBACTER JEJUNI SUBSP. JEJUNI
    Organism Taxid: 192222
    Strain: NCTC 11168
    Synonym: DHDPS

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 37)

Asymmetric/Biological Unit (7, 37)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2EDO2Ligand/Ion1,2-ETHANEDIOL
3FMT1Ligand/IonFORMIC ACID
4MCL4Mod. Amino AcidNZ-(1-CARBOXYETHYL)-LYSINE
5MG1Ligand/IonMAGNESIUM ION
6MSE27Mod. Amino AcidSELENOMETHIONINE
7PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:7BINDING SITE FOR RESIDUE EDO A 301
2AC2SOFTWAREGLU B:287 , HOH B:434 , HOH B:484 , HOH B:516 , HOH B:971 , HOH B:972BINDING SITE FOR RESIDUE MG B 301
3AC3SOFTWAREASP B:238 , GLU B:239 , TYR B:241 , ASN B:242 , LYS B:292BINDING SITE FOR RESIDUE FMT B 302
4AC4SOFTWAREGLN B:116 , SER B:148 , ASP B:150 , THR B:151 , HOH B:828 , HOH B:983BINDING SITE FOR RESIDUE PEG B 303
5AC5SOFTWAREALA B:180 , ASP C:238 , GLU C:239 , TYR C:241 , ASN C:242BINDING SITE FOR RESIDUE EDO C 301
6AC6SOFTWAREGLN D:116 , THR D:151 , LYS D:154 , HOH D:509 , HOH D:749BINDING SITE FOR RESIDUE ACY D 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LER)

(-) 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 3LER)

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHDPS_1PS00665 Dihydrodipicolinate synthase signature 1.DAPA_CAMJE41-58
 
 
 		  4A:41-58
B:41-58
C:41-58
D:41-58
2DHDPS_2PS00666 Dihydrodipicolinate synthase signature 2.DAPA_CAMJE137-168
 
 
 		  4A:137-168
B:137-168
C:137-168
D:137-168

(-) Exons   (0, 0)

(no "Exon" information available for 3LER)

(-) 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
 aligned with DAPA_CAMJE | Q9PPB4 from UniProtKB/Swiss-Prot  Length:298

    Alignment length: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        
           DAPA_CAMJE     1 MDKNIIIGAMTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGADGILSVAPYYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVKEASGNIDKCVDLLAHEPRMMLISGEDAINYPILSNGGKGVISVTSNLLPDMISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAMYLAGLIESLEFRLPLCSPSKENFAKIEEVMKKYKIKGF 298
               SCOP domains d3lera_ A: Dihydrodipicolinate synthase                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains -3lerA00 A:2-298 Aldolase class I                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee....ee..eehhhhhhhhhhhhhh....eee......hhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------DHDPS_1           ------------------------------------------------------------------------------DHDPS_2  PDB: A:137-168         ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ler 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        
                            |       10-MSE                                                                                                                                                     166-MCL            185-MSE                         217-MSE                                    260-MSE                       290-MSE    
                            1-MSE                                                                                                                                                                                  186-MSE                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:298
 aligned with DAPA_CAMJE | Q9PPB4 from UniProtKB/Swiss-Prot  Length:298

    Alignment length: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        
           DAPA_CAMJE     1 MDKNIIIGAMTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGADGILSVAPYYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVKEASGNIDKCVDLLAHEPRMMLISGEDAINYPILSNGGKGVISVTSNLLPDMISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAMYLAGLIESLEFRLPLCSPSKENFAKIEEVMKKYKIKGF 298
               SCOP domains d3lerb_ B: Dihydrodipicolinate synthase                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains -3lerB00 B:2-298 Aldolase class I                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee....ee..eehhhhhhhhhhhhhh....eee...........hhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------DHDPS_1           ------------------------------------------------------------------------------DHDPS_2  PDB: B:137-168         ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ler B   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        
                            1-MSE   10-MSE                                                                                                                                                     166-MCL            185-MSE                         217-MSE                                    260-MSE                       290-MSE    
                                                                                                                                                                                                                   186-MSE                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:296
 aligned with DAPA_CAMJE | Q9PPB4 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:296
                                    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      
           DAPA_CAMJE     3 KNIIIGAMTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGADGILSVAPYYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVKEASGNIDKCVDLLAHEPRMMLISGEDAINYPILSNGGKGVISVTSNLLPDMISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAMYLAGLIESLEFRLPLCSPSKENFAKIEEVMKKYKIKGF 298
               SCOP domains d3lerc_ C: Dihydrodipicolinate synthase                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3lerC00 C:3-298 Aldolase class I                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....ee..eehhhhhhhhhhhhhh....eee......hhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhh.....eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------DHDPS_1           ------------------------------------------------------------------------------DHDPS_2  PDB: C:137-168         ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ler 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      
                                  10-MSE                                                                                                                                                     166-MCL            185-MSE                         217-MSE                                    260-MSE                       290-MSE    
                                                                                                                                                                                                                 186-MSE                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:298
 aligned with DAPA_CAMJE | Q9PPB4 from UniProtKB/Swiss-Prot  Length:298

    Alignment length: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        
           DAPA_CAMJE     1 MDKNIIIGAMTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGADGILSVAPYYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVKEASGNIDKCVDLLAHEPRMMLISGEDAINYPILSNGGKGVISVTSNLLPDMISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAMYLAGLIESLEFRLPLCSPSKENFAKIEEVMKKYKIKGF 298
               SCOP domains d3lerd_ D: Dihydrodipicolinate synthase                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains -3lerD00 D:2-298 Aldolase class I                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee....ee..eehhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------DHDPS_1           ------------------------------------------------------------------------------DHDPS_2  PDB: D:137-168         ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ler D   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        
                            1-MSE   10-MSE                                                                                                                                                     166-MCL            185-MSE                         217-MSE                                    260-MSE                       290-MSE    
                                                                                                                                                                                                                   186-MSE
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3LER)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (DAPA_CAMJE | Q9PPB4)
molecular function
    GO:0008840    4-hydroxy-tetrahydrodipicolinate synthase    Catalysis of the reaction: pyruvate + L-aspartate-4-semialdehyde = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0019877    diaminopimelate biosynthetic process    The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls.
    GO:0009085    lysine biosynthetic process    The chemical reactions and pathways resulting in the formation of lysine, 2,6-diaminohexanoic acid.
    GO:0009089    lysine biosynthetic process via diaminopimelate    The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DAPA_CAMJE | Q9PPB4: 3m5v 4ly8 4m19 4mlj 4mlr 4r53 5f1u 5f1v

(-) Related Entries Specified in the PDB File

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