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(-) Description

Title :  CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM BACILLUS CLAUSII
 
Authors :  A. A. Fedorov, E. V. Fedorov, J. M. Sauder, S. K. Burley, J. A. Gerlt, S. C York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  21 Aug 08  (Deposition) - 02 Sep 08  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Nysgrc, Target 9375C, Operon, Dihydrodipicolinate Synthase, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Fedorov, E. V. Fedorov, J. M. Sauder, S. K. Burley, J. A. Gerlt, S. C. Almo
Crystal Structure Of Dihydrodipicolinate Synthase From Bacillus Clausii
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIHYDRODIPICOLINATE SYNTHASE
    Chains: A, B
    EC Number: 4.2.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ABC3015
    Organism Scientific: BACILLUS CLAUSII KSM-K16
    Organism Taxid: 66692

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3E96)

(-) Sites  (0, 0)

(no "Site" information available for 3E96)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E96)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:280 -Pro A:281
2Ala B:280 -Pro B:281

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E96)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3E96)

(-) Exons   (0, 0)

(no "Exon" information available for 3E96)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:296
 aligned with Q5WDL1_BACSK | Q5WDL1 from UniProtKB/TrEMBL  Length:306

    Alignment length:296
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294      
         Q5WDL1_BACSK     5 PLAKALETISGIPITPFRKSDGSIDWHHYKETVDRIVDNGIDVIVPCGNTSEFYALSLEEAKEEVRRTVEYVHGRALVVAGIGYATSTAIELGNAAKAAGADAVMIHMPIHPYVTAGGVYAYFRDIIEALDFPSLVYFKDPEISDRVLVDLAPLQNLVGVKYAINDLPRFAKVVRSIPEEHQIAWICGTAEKWAPFFWHAGAKGFTSGLVNLLPQKAVEMLEALRNNDNDAVWRIWEDIVPFEDLRGKYNQGNNVVVIKEAMEMLRQNAGVTRAPVNELSNEDKQLVTELLSSWKL 300
               SCOP domains d3e96a_ A: automated matches                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3e96A00 A:7-302 Aldolase class I                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..eee.............hhhhhhhhhhhhhh....ee...hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhh..eeeee......hhhhhhhh....eeeeee...hhhhhhhhhhhhhhhhh.eeee.....hhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..............hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e96 A   7 PLAKALETISGIPITPFRKSDGSIDWHHYKETVDRIVDNGIDVIVPCGNTSEFYALSLEEAKEEVRRTVEYVHGRALVVAGIGYATSTAIELGNAAKAAGADAVMIHMPIHPYVTAGGVYAYFRDIIEALDFPSLVYFKDPEISDRVLVDLAPLQNLVGVKYAINDLPRFAKVVRSIPEEHQIAWICGTAEKWAPFFWHAGAKGFTSGLVNLLPQKAVEMLEALRNNDNDAVWRIWEDIVPFEDLRGKYNQGNNVVVIKEAMEMLRQNAGVTRAPVNELSNEDKQLVTELLSSWKL 302
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296      


Chain B from PDB  Type:PROTEIN  Length:300
 aligned with Q5WDL1_BACSK | Q5WDL1 from UniProtKB/TrEMBL  Length:306

    Alignment length:300
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305
         Q5WDL1_BACSK     6 LAKALETISGIPITPFRKSDGSIDWHHYKETVDRIVDNGIDVIVPCGNTSEFYALSLEEAKEEVRRTVEYVHGRALVVAGIGYATSTAIELGNAAKAAGADAVMIHMPIHPYVTAGGVYAYFRDIIEALDFPSLVYFKDPEISDRVLVDLAPLQNLVGVKYAINDLPRFAKVVRSIPEEHQIAWICGTAEKWAPFFWHAGAKGFTSGLVNLLPQKAVEMLEALRNNDNDAVWRIWEDIVPFEDLRGKYNQGNNVVVIKEAMEMLRQNAGVTRAPVNELSNEDKQLVTELLSSWKLLQPTK 305
               SCOP domains d3e96b_ B: automated matches                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 3e96B00 B:8-307 Aldolase class I                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eee.............hhhhhhhhhhhhhh....ee.......hhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhh..eeeee......hhhhhhhh....eeeeee...hhhhhhhhhhhhhhhhh.eeee.....hhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..............hhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3e96 B   8 LAKALETISGIPITPFRKSDGSIDWHHYKETVDRIVDNGIDVIVPCGNTSEFYALSLEEAKEEVRRTVEYVHGRALVVAGIGYATSTAIELGNAAKAAGADAVMIHMPIHPYVTAGGVYAYFRDIIEALDFPSLVYFKDPEISDRVLVDLAPLQNLVGVKYAINDLPRFAKVVRSIPEEHQIAWICGTAEKWAPFFWHAGAKGFTSGLVNLLPQKAVEMLEALRNNDNDAVWRIWEDIVPFEDLRGKYNQGNNVVVIKEAMEMLRQNAGVTRAPVNELSNEDKQLVTELLSSWKLLQPTK 307
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E96)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5WDL1_BACSK | Q5WDL1)
molecular function
    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: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.

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  Sites
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  Cis Peptide Bonds
    Ala A:280 - Pro A:281   [ RasMol ]  
    Ala B:280 - Pro B:281   [ RasMol ]  
 

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  3e96
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 Related Entries

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