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(-) Description

Title :  CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM BARTONELLA HENSELAE
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S B. L. Staker, J. Abendroth, B. Sankaran
Date :  17 Jun 11  (Deposition) - 29 Jun 11  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Tim Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. F. Naqvi, B. L. Staker, R. C. Dobson, D. Serbzhinskiy, B. Sankaran, P. J. Myler, A. O. Hudson
Cloning, Expression, Purification, Crystallization And X-Ra Diffraction Analysis Of Dihydrodipicolinate Synthase From The Human Pathogenic Bacterium Bartonella Henselae Strain Houston-1 At 2. 1 Angstrom Resolution.
Acta Crystallogr F Struct V. 72 2 2016 Biol Commun
PubMed-ID: 26750477  |  Reference-DOI: 10.1107/S2053230X15023213

(-) Compounds

Molecule 1 - DIHYDRODIPICOLINATE SYNTHASE
    ChainsA, B, C, D
    EC Number4.2.1.52
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidAVA0421
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneDAPA, BH05000
    Organism ScientificBARTONELLA HENSELAE
    Organism Taxid38323
    StrainHOUSTON-1
    SynonymDHDPS

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric/Biological Unit (1, 9)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:184 , PHE A:186 , VAL A:187 , GLN A:188 , GLY A:203 , VAL A:205BINDING SITE FOR RESIDUE EDO A 801
2AC2SOFTWARESER A:52 , PRO A:53 , TYR A:110 , HOH A:320 , HOH A:422BINDING SITE FOR RESIDUE EDO A 802
3AC3SOFTWARETYR A:120 , ASP A:154BINDING SITE FOR RESIDUE EDO A 803
4AC4SOFTWAREALA B:168 , HOH B:469BINDING SITE FOR RESIDUE EDO B 801
5AC5SOFTWAREGLN B:116 , TYR B:120 , ASP B:154BINDING SITE FOR RESIDUE EDO B 802
6AC6SOFTWAREASN C:115 , GLN C:116 , HOH C:370 , HOH C:395BINDING SITE FOR RESIDUE EDO C 801
7AC7SOFTWAREARG C:117 , THR C:151 , ASP C:154BINDING SITE FOR RESIDUE EDO C 802
8AC8SOFTWAREASP D:193 , LEU D:222 , HIS D:223 , ASN D:238 , ASN D:245BINDING SITE FOR RESIDUE EDO D 801
9AC9SOFTWARELEU D:264BINDING SITE FOR RESIDUE EDO D 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SI9)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ser A:253 -Pro A:254
2Ser A:273 -Pro A:274
3Ser B:253 -Pro B:254
4Ser B:273 -Pro B:274
5Ser C:253 -Pro C:254
6Ser C:273 -Pro C:274
7Ser D:253 -Pro D:254
8Ser D:273 -Pro D:274

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SI9)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHDPS_2PS00666 Dihydrodipicolinate synthase signature 2.DAPA_BARHE133-164
 
 
 
  4A:137-168
B:137-168
C:137-168
D:137-168

(-) Exons   (0, 0)

(no "Exon" information available for 3SI9)

(-) 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:294
 aligned with DAPA_BARHE | Q6G468 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:294
                             1                                                                                                                                                                                                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289    
           DAPA_BARHE     - -MLKGAVTALITPFDDNGAIDEKAFCNFVEWQITQGINGVSPVGTTGESPTLTHEEHKRIIELCVEQVAKRVPVVAGAGSNSTSEAVELAKHAEKAGADAVLVVTPYYNRPNQRGLYTHFSSIAKAISIPIIIYNIPSRSVIDMAVETMRDLCRDFKNIIGVKDATGKIERASEQREKCGKDFVQLSGDDCTALGFNAHGGVGCISVSSNVAPKLCAQLHAACLCSDYKTALKLNDLLMPLNRAVFIEPSPAGIKYAAAKLGLCGTIVRSPIVPLSDTTKKIIDEALYHAGLLK 293
               SCOP domains d3si9a_ A: automated matches                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee...........hhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhhhh..eeeeee....hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------DHDPS_2  PDB: A:137-168         --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3si9 A   4 SMLKGAVTALITPFDDNGAIDEKAFCNFVEWQITQGINGVSPVGTTGESPTLTHEEHKRIIELCVEQVAKRVPVVAGAGSNSTSEAVELAKHAEKAGADAVLVVTPYYNRPNQRGLYTHFSSIAKAISIPIIIYNIPSRSVIDMAVETMRDLCRDFKNIIGVKDATGKIERASEQREKCGKDFVQLSGDDCTALGFNAHGGVGCISVSSNVAPKLCAQLHAACLCSDYKTALKLNDLLMPLNRAVFIEPSPAGIKYAAAKLGLCGTIVRSPIVPLSDTTKKIIDEALYHAGLLK 297
                                    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 B from PDB  Type:PROTEIN  Length:293
 aligned with DAPA_BARHE | Q6G468 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:293
                             1                                                                                                                                                                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289   
           DAPA_BARHE     - -MLKGAVTALITPFDDNGAIDEKAFCNFVEWQITQGINGVSPVGTTGESPTLTHEEHKRIIELCVEQVAKRVPVVAGAGSNSTSEAVELAKHAEKAGADAVLVVTPYYNRPNQRGLYTHFSSIAKAISIPIIIYNIPSRSVIDMAVETMRDLCRDFKNIIGVKDATGKIERASEQREKCGKDFVQLSGDDCTALGFNAHGGVGCISVSSNVAPKLCAQLHAACLCSDYKTALKLNDLLMPLNRAVFIEPSPAGIKYAAAKLGLCGTIVRSPIVPLSDTTKKIIDEALYHAGLL 292
               SCOP domains d3si9b_ B: automated matches                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...........hhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhhhh..eeeeee....hhhhhhhhhhhh...eeee....hhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------DHDPS_2  PDB: B:137-168         -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3si9 B   4 SMLKGAVTALITPFDDNGAIDEKAFCNFVEWQITQGINGVSPVGTTGESPTLTHEEHKRIIELCVEQVAKRVPVVAGAGSNSTSEAVELAKHAEKAGADAVLVVTPYYNRPNQRGLYTHFSSIAKAISIPIIIYNIPSRSVIDMAVETMRDLCRDFKNIIGVKDATGKIERASEQREKCGKDFVQLSGDDCTALGFNAHGGVGCISVSSNVAPKLCAQLHAACLCSDYKTALKLNDLLMPLNRAVFIEPSPAGIKYAAAKLGLCGTIVRSPIVPLSDTTKKIIDEALYHAGLL 296
                                    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:293
 aligned with DAPA_BARHE | Q6G468 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:293
                             1                                                                                                                                                                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289   
           DAPA_BARHE     - -MLKGAVTALITPFDDNGAIDEKAFCNFVEWQITQGINGVSPVGTTGESPTLTHEEHKRIIELCVEQVAKRVPVVAGAGSNSTSEAVELAKHAEKAGADAVLVVTPYYNRPNQRGLYTHFSSIAKAISIPIIIYNIPSRSVIDMAVETMRDLCRDFKNIIGVKDATGKIERASEQREKCGKDFVQLSGDDCTALGFNAHGGVGCISVSSNVAPKLCAQLHAACLCSDYKTALKLNDLLMPLNRAVFIEPSPAGIKYAAAKLGLCGTIVRSPIVPLSDTTKKIIDEALYHAGLL 292
               SCOP domains d3si9c_ C: automated matches                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...........hhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhhhh..eeeeee....hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------DHDPS_2  PDB: C:137-168         -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3si9 C   4 SMLKGAVTALITPFDDNGAIDEKAFCNFVEWQITQGINGVSPVGTTGESPTLTHEEHKRIIELCVEQVAKRVPVVAGAGSNSTSEAVELAKHAEKAGADAVLVVTPYYNRPNQRGLYTHFSSIAKAISIPIIIYNIPSRSVIDMAVETMRDLCRDFKNIIGVKDATGKIERASEQREKCGKDFVQLSGDDCTALGFNAHGGVGCISVSSNVAPKLCAQLHAACLCSDYKTALKLNDLLMPLNRAVFIEPSPAGIKYAAAKLGLCGTIVRSPIVPLSDTTKKIIDEALYHAGLL 296
                                    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 D from PDB  Type:PROTEIN  Length:294
 aligned with DAPA_BARHE | Q6G468 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:294
                             1                                                                                                                                                                                                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289    
           DAPA_BARHE     - -MLKGAVTALITPFDDNGAIDEKAFCNFVEWQITQGINGVSPVGTTGESPTLTHEEHKRIIELCVEQVAKRVPVVAGAGSNSTSEAVELAKHAEKAGADAVLVVTPYYNRPNQRGLYTHFSSIAKAISIPIIIYNIPSRSVIDMAVETMRDLCRDFKNIIGVKDATGKIERASEQREKCGKDFVQLSGDDCTALGFNAHGGVGCISVSSNVAPKLCAQLHAACLCSDYKTALKLNDLLMPLNRAVFIEPSPAGIKYAAAKLGLCGTIVRSPIVPLSDTTKKIIDEALYHAGLLK 293
               SCOP domains d3si9d_ D: automated matches                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -DHDPS-3si9D01 D:5-294                                                                                                                                                                                                                                                                             --- Pfam domains (1)
           Pfam domains (2) -DHDPS-3si9D02 D:5-294                                                                                                                                                                                                                                                                             --- Pfam domains (2)
           Pfam domains (3) -DHDPS-3si9D03 D:5-294                                                                                                                                                                                                                                                                             --- Pfam domains (3)
           Pfam domains (4) -DHDPS-3si9D04 D:5-294                                                                                                                                                                                                                                                                             --- Pfam domains (4)
         Sec.struct. author ....eeeee...........hhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhhhh..eeeeee....hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------DHDPS_2  PDB: D:137-168         --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3si9 D   4 SMLKGAVTALITPFDDNGAIDEKAFCNFVEWQITQGINGVSPVGTTGESPTLTHEEHKRIIELCVEQVAKRVPVVAGAGSNSTSEAVELAKHAEKAGADAVLVVTPYYNRPNQRGLYTHFSSIAKAISIPIIIYNIPSRSVIDMAVETMRDLCRDFKNIIGVKDATGKIERASEQREKCGKDFVQLSGDDCTALGFNAHGGVGCISVSSNVAPKLCAQLHAACLCSDYKTALKLNDLLMPLNRAVFIEPSPAGIKYAAAKLGLCGTIVRSPIVPLSDTTKKIIDEALYHAGLLK 297
                                    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    

   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  (1, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SI9)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (DAPA_BARHE | Q6G468)
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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