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(-) Description

Title :  CRYSTAL STRUCTURE OF DIAMINOPIMELATE EPIMERASE IN COMPLEX WITH AN IRREVERSIBLE INHIBITOR DL-AZIDAP
 
Authors :  B. Pillai, M. M. Cherney, C. M. Diaper, A. Sutherland, J. S. Blanchard, J. C. Vederas, M. N. James
Date :  02 Apr 06  (Deposition) - 16 May 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Enzyme-Inhibitor Complex, Covalently Bound Inhibitor, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Pillai, M. M. Cherney, C. M. Diaper, A. Sutherland, J. S. Blanchard, J. C. Vederas, M. N. James
Structural Insights Into Stereochemical Inversion By Diaminopimelate Epimerase: An Antibacterial Drug Target.
Proc. Natl. Acad. Sci. Usa V. 103 8668 2006
PubMed-ID: 16723397  |  Reference-DOI: 10.1073/PNAS.0602537103
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIAMINOPIMELATE EPIMERASE
    Chains: A
    EC Number: 5.1.1.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DAPF
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727
    Synonym: DAP EPIMERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2ZDR1Ligand/Ion(2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:11 , GLN A:44 , ASN A:64 , VAL A:70 , GLN A:72 , CYS A:73 , GLY A:74 , ASN A:75 , ASN A:157 , ASN A:190 , GLU A:208 , ARG A:209 , CYS A:217 , GLY A:218 , SER A:219BINDING SITE FOR RESIDUE ZDR A 700
2AC2SOFTWAREPHE A:24 , PHE A:25 , ARG A:61 , HOH A:362 , HOH A:439BINDING SITE FOR RESIDUE ACY A 579
3AC3SOFTWARETYR A:139 , ILE A:140 , ARG A:184 , HOH A:349 , HOH A:444BINDING SITE FOR RESIDUE ACY A 580

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ile A:128 -Pro A:129

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DAP_EPIMERASEPS01326 Diaminopimelate epimerase signature.DAPF_HAEIN64-78  1A:64-78

(-) Exons   (0, 0)

(no "Exon" information available for 2GKJ)

(-) 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:274
 aligned with DAPF_HAEIN | P44859 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:274
                                    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    
           DAPF_HAEIN     1 MQFSKMHGLGNDFVVVDGVTQNVFFTPETIRRLANRHCGIGFDQLLIVEAPYDPELDFHYRIFNADGSEVSQCGNGARCFARFVTLKGLTNKKDISVSTQKGNMVLTVKDDNQIRVNMGEPIWEPAKIPFTANKFEKNYILRTDIQTVLCGAVSMGNPHCVVQVDDIQTANVEQLGPLLESHERFPERVNAGFMQIINKEHIKLRVYERGAGETQACGSGACAAVAVGIMQGLLNNNVQVDLPGGSLMIEWNGVGHPLYMTGEATHIYDGFITL 274
               SCOP domains d2gkja1 A:1-130 Diaminopimelate epimerase                                                                                         d2gkja2 A:131-274 Diaminopimelate epimerase                                                                                                      SCOP domains
               CATH domains 2gkjA01 A:1-114,A:262-274 Diaminopimelate Epimerase; Chain A, domain 1                                            2gkjA02                  ----------2gkjA02 A:115-139,A:150-261 Diaminopimelate Epimerase; Chain A, domain 1                                        2gkjA01       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeeee........hhhhhhhhhh........eeeeee........eeeeeee....ee..hhhhhhhhhhhhhhh......eeeee.....eeeee.....eeee......hhhhh..........eeee....eeeeeeee...eeeeee.......hhhhhhhhhhh........eeeeeeeee..eeeeeeee...ee...hhhhhhhhhhhhhhh.....eeeeee..eeeeeee......eeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------DAP_EPIMERASE  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gkj A   1 MQFSKMHGLGNDFVVVDGVTQNVFFTPETIRRLANRHCGIGFDQLLIVEAPYDPELDFHYRIFNADGSEVSQCGNGARCFARFVTLKGLTNKKDISVSTQKGNMVLTVKDDNQIRVNMGEPIWEPAKIPFTANKFEKNYILRTDIQTVLCGAVSMGNPHCVVQVDDIQTANVEQLGPLLESHERFPERVNAGFMQIINKEHIKLRVYERGAGETQACGSGACAAVAVGIMQGLLNNNVQVDLPGGSLMIEWNGVGHPLYMTGEATHIYDGFITL 274
                                    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
   Legend:   → Mismatch (orange background)
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  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) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GKJ)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DAPF_HAEIN | P44859)
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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  5.1.1.7
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DAPF_HAEIN | P44859: 1bwz 1gqz 2gke 2q9h 2q9j

(-) Related Entries Specified in the PDB File

2gke CRYSTAL STRUCTURE OF DIAMINOPIMELATE EPIMERASE IN COMPLEX WITH AN IRREVERSIBLE INHIBITOR LL-AZIDAP