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(-) Description

Title :  STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM CLOSTRIDIUM BOTULINUM
 
Authors :  R. C. J. Dobson, S. Atkinson, M. A. Perugini
Date :  22 Aug 09  (Deposition) - 22 Sep 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.23
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Clostridium Botulinum, Dihydrodipicolinate Synthase, Amino-Acid Biosynthesis, Diaminopimelate Biosynthesis, Lyase, Lysine Biosynthesis, Schiff Base (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S Atkinson, R. C. J. Dobson, M. A. Perugini
Structure Of Cbot-Dhdps
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIHYDRODIPICOLINATE SYNTHASE
    Chains: A
    EC Number: 4.2.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21-DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DAPA
    Organism Scientific: CLOSTRIDIUM BOTULINUM A STR. HALL
    Organism Taxid: 441771
    Strain: HALL STRAIN A

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3MLT1Ligand/IonMALATE ION
4NA1Ligand/IonSODIUM ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL8Ligand/IonGLYCEROL
3MLT4Ligand/IonMALATE ION
4NA-1Ligand/IonSODIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:10 , GLY A:44 , THR A:45 , THR A:46 , LEU A:102 , TYR A:134 , ARG A:139 , LYS A:162 , ILE A:204 , PHE A:245 , ASN A:249 , HOH A:492 , HOH A:556 , HOH A:583BINDING SITE FOR RESIDUE MLT A 300
2AC2SOFTWARECYS A:153 , ASP A:155 , ILE A:158 , HOH A:363 , HOH A:402BINDING SITE FOR RESIDUE NA A 301
3AC3SOFTWAREGLY A:166 , ASN A:167 , ILE A:168BINDING SITE FOR RESIDUE CL A 302
4AC4SOFTWARETYR A:107 , TYR A:108 , ARG A:139 , THR A:140BINDING SITE FOR RESIDUE CL A 303
5AC5SOFTWAREASN A:258 , ASP A:266 , LEU A:267 , HOH A:331 , HOH A:471BINDING SITE FOR RESIDUE GOL A 294
6AC6SOFTWARESER A:95 , MET A:260 , LEU A:291 , HOH A:359 , HOH A:377 , HOH A:504BINDING SITE FOR RESIDUE GOL A 295

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:249 -Pro A:250
2Leu A:269 -Pro A:270

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3IRD)

(-) Sequences/Alignments

Asymmetric 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:291
 aligned with A5I6N2_CLOBH | A5I6N2 from UniProtKB/TrEMBL  Length:292

    Alignment length:291
                                    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 
         A5I6N2_CLOBH     2 SIFKGSGVAIITPFTNTGVDFDKLSELIEWHIKSKTDAIIVCGTTGEATTMTETERKETIKFVIDKVNKRIPVIAGTGSNNTAASIAMSKWAESIGVDGLLVITPYYNKTTQKGLVKHFKAVSDAVSTPIIIYNVPGRTGLNITPGTLKELCEDKNIVAVKEASGNISQIAQIKALCGDKLDIYSGNDDQIIPILALGGIGVISVLANVIPEDVHNMCELYLNGKVNEALKIQLDSLALTNALFIETNPIPVKTAMNLMNMKVGDLRLPLCEMNENNLEILKKELKAYNLM 292
               SCOP domains d3irda_ A: Dihydrodipicolinate synthase                                                                                                                                                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..........hhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhh....eeeeee...hhhhhhhhhhhhhhhheeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ird A   2 SIFKGSGVAIITPFTNTGVDFDKLSELIEWHIKSKTDAIIVCGTTGEATTMTETERKETIKFVIDKVNKRIPVIAGTGSNNTAASIAMSKWAESIGVDGLLVITPYYNKTTQKGLVKHFKAVSDAVSTPIIIYNVPGRTGLNITPGTLKELCEDKNIVAVKEASGNISQIAQIKALCGDKLDIYSGNDDQIIPILALGGIGVISVLANVIPEDVHNMCELYLNGKVNEALKIQLDSLALTNALFIETNPIPVKTAMNLMNMKVGDLRLPLCEMNENNLEILKKELKAYNLM 292
                                    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
   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, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (A5I6N2_CLOBH | A5I6N2)
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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3bi8 EARLIER VERSION OF THIS STRUCTURE