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(-) Description

Title :  CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM HAHELLA CHEJUENSIS AT 1.5A RESOLUTION
 
Authors :  B. S. Kang, M. H. Kim, G. H. Kim, K. J. Kim
Date :  29 Sep 07  (Deposition) - 23 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Beta Barrel, Amino-Acid Biosynthesis, Diaminopimelate Biosynthesis, Lyase, Lysine Biosynthesis, Schiff Base (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. S. Kang, M. H. Kim, G. H. Kim, K. J. Kim
Crystal Structure Of Dihydrodipicolinate Synthase From Hahella Chejuensis At 1. 5A Resolution
To Be Published
PubMed: search

(-) 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: PET30A
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: HAHELLA CHEJUENSIS
    Organism Taxid: 158327

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1EOH1Ligand/IonETHANOL
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:660 , HOH A:667 , HOH A:833 , HOH A:868 , HOH A:907 , HOH B:451BINDING SITE FOR RESIDUE MG A 298
2AC2SOFTWAREGLU A:20 , GLU A:54 , ARG A:57 , HOH A:557 , HOH A:700BINDING SITE FOR RESIDUE EOH A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2RFG)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Ser A:247 -Pro A:248
2Leu A:267 -Pro A:268
3Tyr A:288 -Arg A:289
4Ser B:247 -Pro B:248
5Leu B:267 -Pro B:268
6Met C:1 -Phe C:2
7Ser C:247 -Pro C:248
8Leu C:267 -Pro C:268
9Ser D:247 -Pro D:248
10Leu D:267 -Pro D:268

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RFG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2RFG)

(-) Exons   (0, 0)

(no "Exon" information available for 2RFG)

(-) 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:289
 aligned with Q2S9K4_HAHCH | Q2S9K4 from UniProtKB/TrEMBL  Length:289

    Alignment length:289
                                    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         
         Q2S9K4_HAHCH     1 MFRGSLIAMITPFINGQVDEKALAGLVDWQIKHGAHGLVPVGTTGESPTLTEEEHKRVVALVAEQAQGRVPVIAGAGSNNPVEAVRYAQHAQQAGADAVLCVAGYYNRPSQEGLYQHFKMVHDAIDIPIIVYNIPPRAVVDIKPETMARLAALPRIVGVKDATTDLARISRERMLINKPFSFLSGDDMTAIAYNASGGQGCISVSANIAPALYGQMQTATLQGDFREALRIHDLLAPLHEALFREPSPAGAKYAASLLGLCNEECRLPIVPLSEQTKSDIKNIINELYR 289
               SCOP domains d2rfga_ A: automated matches                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2rfgA00 A:1-289 Aldolase class I                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....ee..eehhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhh...eeeeee.....hhhhhhhh......eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh..............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rfg A   1 MFRGSLIAMITPFINGQVDEKALAGLVDWQIKHGAHGLVPVGTTGESPTLTEEEHKRVVALVAEQAQGRVPVIAGAGSNNPVEAVRYAQHAQQAGADAVLCVAGYYNRPSQEGLYQHFKMVHDAIDIPIIVYNIPPRAVVDIKPETMARLAALPRIVGVKDATTDLARISRERMLINKPFSFLSGDDMTAIAYNASGGQGCISVSANIAPALYGQMQTATLQGDFREALRIHDLLAPLHEALFREPSPAGAKYAASLLGLCNEECRLPIVPLSEQTKSDIKNIINELYR 289
                                    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         


Chain B from PDB  Type:PROTEIN  Length:297
 aligned with Q2S9K4_HAHCH | Q2S9K4 from UniProtKB/TrEMBL  Length:289

    Alignment length:297
                                                                                                                                                                                                                                                                                                                          289        
                                    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        |-       
         Q2S9K4_HAHCH     1 MFRGSLIAMITPFINGQVDEKALAGLVDWQIKHGAHGLVPVGTTGESPTLTEEEHKRVVALVAEQAQGRVPVIAGAGSNNPVEAVRYAQHAQQAGADAVLCVAGYYNRPSQEGLYQHFKMVHDAIDIPIIVYNIPPRAVVDIKPETMARLAALPRIVGVKDATTDLARISRERMLINKPFSFLSGDDMTAIAYNASGGQGCISVSANIAPALYGQMQTATLQGDFREALRIHDLLAPLHEALFREPSPAGAKYAASLLGLCNEECRLPIVPLSEQTKSDIKNIINELYR--------   -
               SCOP domains d2rfgb_ B: automated matches                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2rfgB00 B:1-297 Aldolase class I                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....ee..eehhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhh...eeeeee.....hhhhhhhh......eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rfg B   1 MFRGSLIAMITPFINGQVDEKALAGLVDWQIKHGAHGLVPVGTTGESPTLTEEEHKRVVALVAEQAQGRVPVIAGAGSNNPVEAVRYAQHAQQAGADAVLCVAGYYNRPSQEGLYQHFKMVHDAIDIPIIVYNIPPRAVVDIKPETMARLAALPRIVGVKDATTDLARISRERMLINKPFSFLSGDDMTAIAYNASGGQGCISVSANIAPALYGQMQTATLQGDFREALRIHDLLAPLHEALFREPSPAGAKYAASLLGLCNEECRLPIVPLSEQTKSDIKNIINELYRLEHHHHHH 297
                                    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       


Chain C from PDB  Type:PROTEIN  Length:289
 aligned with Q2S9K4_HAHCH | Q2S9K4 from UniProtKB/TrEMBL  Length:289

    Alignment length:289
                                    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         
         Q2S9K4_HAHCH     1 MFRGSLIAMITPFINGQVDEKALAGLVDWQIKHGAHGLVPVGTTGESPTLTEEEHKRVVALVAEQAQGRVPVIAGAGSNNPVEAVRYAQHAQQAGADAVLCVAGYYNRPSQEGLYQHFKMVHDAIDIPIIVYNIPPRAVVDIKPETMARLAALPRIVGVKDATTDLARISRERMLINKPFSFLSGDDMTAIAYNASGGQGCISVSANIAPALYGQMQTATLQGDFREALRIHDLLAPLHEALFREPSPAGAKYAASLLGLCNEECRLPIVPLSEQTKSDIKNIINELYR 289
               SCOP domains d2rfgc_ C: automated matches                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2rfgC00 C:1-289 Aldolase class I                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....ee..eehhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhh...eeeeee.....hhhhhhhh......eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh..............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rfg C   1 MFRGSLIAMITPFINGQVDEKALAGLVDWQIKHGAHGLVPVGTTGESPTLTEEEHKRVVALVAEQAQGRVPVIAGAGSNNPVEAVRYAQHAQQAGADAVLCVAGYYNRPSQEGLYQHFKMVHDAIDIPIIVYNIPPRAVVDIKPETMARLAALPRIVGVKDATTDLARISRERMLINKPFSFLSGDDMTAIAYNASGGQGCISVSANIAPALYGQMQTATLQGDFREALRIHDLLAPLHEALFREPSPAGAKYAASLLGLCNEECRLPIVPLSEQTKSDIKNIINELYR 289
                                    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         


Chain D from PDB  Type:PROTEIN  Length:289
 aligned with Q2S9K4_HAHCH | Q2S9K4 from UniProtKB/TrEMBL  Length:289

    Alignment length:289
                                    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         
         Q2S9K4_HAHCH     1 MFRGSLIAMITPFINGQVDEKALAGLVDWQIKHGAHGLVPVGTTGESPTLTEEEHKRVVALVAEQAQGRVPVIAGAGSNNPVEAVRYAQHAQQAGADAVLCVAGYYNRPSQEGLYQHFKMVHDAIDIPIIVYNIPPRAVVDIKPETMARLAALPRIVGVKDATTDLARISRERMLINKPFSFLSGDDMTAIAYNASGGQGCISVSANIAPALYGQMQTATLQGDFREALRIHDLLAPLHEALFREPSPAGAKYAASLLGLCNEECRLPIVPLSEQTKSDIKNIINELYR 289
               SCOP domains d2rfgd_ D: automated matches                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2rfgD00 D:1-289 Aldolase class I                                                                                                                                                                                                                                                                  CATH domains
           Pfam domains (1) DHDPS-2rfgD01 D:1-288                                                                                                                                                                                                                                                                           - Pfam domains (1)
           Pfam domains (2) DHDPS-2rfgD02 D:1-288                                                                                                                                                                                                                                                                           - Pfam domains (2)
           Pfam domains (3) DHDPS-2rfgD03 D:1-288                                                                                                                                                                                                                                                                           - Pfam domains (3)
           Pfam domains (4) DHDPS-2rfgD04 D:1-288                                                                                                                                                                                                                                                                           - Pfam domains (4)
         Sec.struct. author ...eeeee....ee..eehhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhh...eeeeee.....hhhhhhhh......eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh..............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rfg D   1 MFRGSLIAMITPFINGQVDEKALAGLVDWQIKHGAHGLVPVGTTGESPTLTEEEHKRVVALVAEQAQGRVPVIAGAGSNNPVEAVRYAQHAQQAGADAVLCVAGYYNRPSQEGLYQHFKMVHDAIDIPIIVYNIPPRAVVDIKPETMARLAALPRIVGVKDATTDLARISRERMLINKPFSFLSGDDMTAIAYNASGGQGCISVSANIAPALYGQMQTATLQGDFREALRIHDLLAPLHEALFREPSPAGAKYAASLLGLCNEECRLPIVPLSEQTKSDIKNIINELYR 289
                                    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
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q2S9K4_HAHCH | Q2S9K4)
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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