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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTICALLY ACTIVE FORM OF DIAMINOPIMELATE EPIMERASE FROM BACILLUS ANTHRACIS
 
Authors :  M. H. Matho, K. Fukuda, E. Santelli, L. Jaroszewski, R. C. Liddington, D
Date :  08 Feb 07  (Deposition) - 04 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Bacillus Anthracis Diaminopimelate Epimerase, Dap, Lysine Metabolism, Lanthionine, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. H. Matho, K. Fukuda, A. J. Lloyd, E. Santelli, L. Jaroszewski, D. J. Scott, R. C. Liddington, D. Roper
Crystal Structure And Inhibition Of A Catalytically Active Form Of Diaminopimelate Epimerase (Dapf)From Bacillus Anthracis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIAMINOPIMELATE EPIMERASE
    Chains: A, B
    EC Number: 5.1.1.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(ROSETTA)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DAPF
    Organism Scientific: BACILLUS ANTHRACIS STR.
    Organism Taxid: 198094
    Strain: AMES

 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 2OTN)

(-) Sites  (0, 0)

(no "Site" information available for 2OTN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ile A:135 -Pro A:136
2Thr A:143 -Pro A:144
3Ile B:135 -Pro B:136
4Thr B:143 -Pro B:144

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DAP_EPIMERASEPS01326 Diaminopimelate epimerase signature.DAPF_BACAN67-81
 		  2A:67-81
B:67-81

(-) Exons   (0, 0)

(no "Exon" information available for 2OTN)

(-) 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:293
 aligned with DAPF_BACAN | Q81XR2 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:293
                                  1                                                                                                                                                                                                                                                                                              
                                  |  4        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   
           DAPF_BACAN     - ------MSQFSFTKMHGLGNSYIYVNMFEEQIPEEDLALVAEKVSNINTGIGADGMILICPSDVAPVKMRMFNNDGSEGKSCGNGLRCVAKYAYEHKLVEDTVFTIETLAGIVTAEVTVEEGKVTLAKIDMGAPRLTRAEIPMLGEGETPFIRENFLYNNHRYAFTAVSMGNPHAVIFVDDVEQAPLTTLGPVLETHEMFPERVNVEFIEILNEEEMNFRVWERGSGVTQACGTGACAAVVASILNGKMERGKEITVHLAGGDLMIAWTEEGNVLMKGPAEVICRGVYEYKIE 287
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeeee..eeeeeee......hhhhhhhhhhhhhh........eeeeee......eeeeeee....ee.....hhhhhhhhhhhh......eeeeee..eeeeeeeee....eeeeeeeee....hhhhh..........eeeeeee..eeeeeeeee...eeeeee..hhhhh...hhhhhhhh........eeeeeeeee..eeeeeee.........hhhhhhhhhhhhhhh........eeee....eeeeee.....eeeeee.eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------DAP_EPIMERASE  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2otn A  -5 VPRGSHMSQFSFTKMHGLGNSYIYVNMFEEQIPEEDLALVAEKVSNINTGIGADGMILICPSDVAPVKMRMFNNDGSEGKSCGNGLRCVAKYAYEHKLVEDTVFTIETLAGIVTAEVTVEEGKVTLAKIDMGAPRLTRAEIPMLGEGETPFIRENFLYNNHRYAFTAVSMGNPHAVIFVDDVEQAPLTTLGPVLETHEMFPERVNVEFIEILNEEEMNFRVWERGSGVTQACGTGACAAVVASILNGKMERGKEITVHLAGGDLMIAWTEEGNVLMKGPAEVICRGVYEYKIE 287
                                     4        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   


Chain B from PDB  Type:PROTEIN  Length:288
 aligned with DAPF_BACAN | Q81XR2 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:295
                                    1                                                                                                                                                                                                                                                                                              
                                    |2        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     
           DAPF_BACAN     - --------MSQFSFTKMHGLGNSYIYVNMFEEQIPEEDLALVAEKVSNINTGIGADGMILICPSDVAPVKMRMFNNDGSEGKSCGNGLRCVAKYAYEHKLVEDTVFTIETLAGIVTAEVTVEEGKVTLAKIDMGAPRLTRAEIPMLGEGETPFIRENFLYNNHRYAFTAVSMGNPHAVIFVDDVEQAPLTTLGPVLETHEMFPERVNVEFIEILNEEEMNFRVWERGSGVTQACGTGACAAVVASILNGKMERGKEITVHLAGGDLMIAWTEEGNVLMKGPAEVICRGVYEYKIE 287
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------DAP_epimerase-2otnB01 B:160-277                                                                                       ---------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------DAP_epimerase-2otnB02 B:160-277                                                                                       ---------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------DAP_epimerase-2otnB03 B:160-277                                                                                       ---------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------DAP_epimerase-2otnB04 B:160-277                                                                                       ---------- Pfam domains (4)
         Sec.struct. author .......eeeeeeeeeee....eeeeee......hhhhhhhhhhhhhh........eeeeee......eeeeeee...........hhhhhhhhhhhh......eeeee....eeeeeeee....eeeeeee......hhhhh..........eeeeee....eeeeeeee...eeeeee..hhhhh...hhhhhhhh........eeeeeee....eeeeeee..-------hhhhhhhhhhhhhhh........eeee....eeeeee.....eeeeee.eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------DAP_EPIMERASE  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2otn B  -7 GLVPRGSHMSQFSFTKMHGLGNSYIYVNMFEEQIPEEDLALVAEKVSNINTGIGADGMILICPSDVAPVKMRMFNNDGSEGKSCGNGLRCVAKYAYEHKLVEDTVFTIETLAGIVTAEVTVEEGKVTLAKIDMGAPRLTRAEIPMLGEGETPFIRENFLYNNHRYAFTAVSMGNPHAVIFVDDVEQAPLTTLGPVLETHEMFPERVNVEFIEILNEEEMNFRVWER-------CGTGACAAVVASILNGKMERGKEITVHLAGGDLMIAWTEEGNVLMKGPAEVICRGVYEYKIE 287
                                     2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212     |   -   |   232       242       252       262       272       282     
                                                                                                                                                                                                                                                           218     226
   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  (0, 0)

(no "SCOP Domain" information available for 2OTN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OTN)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: DAP_epimerase (14)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DAPF_BACAN | Q81XR2)
molecular function
    GO:0008837    diaminopimelate epimerase activity    Catalysis of the reaction: LL-2,6-diaminopimelate = meso-2,6-diaminopimelate.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
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: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.
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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  Cis Peptide Bonds
    Ile A:135 - Pro A:136   [ RasMol ]  
    Ile B:135 - Pro B:136   [ RasMol ]  
    Thr A:143 - Pro A:144   [ RasMol ]  
    Thr B:143 - Pro B:144   [ RasMol ]  
 

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