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(-) Description

Title :  CRYSTAL STRUCTURE OF DIAMINOPIMELATE EPIMERASE Y268A MUTANT FROM ESCHERICHIA COLI
 
Authors :  L. Hor, R. C. J. Dobson, C. A. Hutton, M. A. Perugini
Date :  24 Dec 12  (Deposition) - 20 Feb 13  (Release) - 17 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dap Epimerase-Like, Isomerase, Cytosol (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Hor, R. C. J. Dobson, M. T. Downton, J. Wagner, C. A. Hutton, M. A. Perugini
Dimerization Of Bacterial Diaminopimelate Epimerase Is Essential For Catalysis
J. Biol. Chem. V. 288 9238 2013
PubMed-ID: 23426375  |  Reference-DOI: 10.1074/JBC.M113.450148

(-) Compounds

Molecule 1 - DIAMINOPIMELATE EPIMERASE
    Chains: A, B
    EC Number: 5.1.1.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DAPF
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: DAP EPIMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 13)

Asymmetric/Biological Unit (1, 13)
No.NameCountTypeFull Name
1IOD13Ligand/IonIODIDE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:79BINDING SITE FOR RESIDUE IOD A 301
02AC2SOFTWAREARG A:78BINDING SITE FOR RESIDUE IOD A 303
03AC3SOFTWAREALA A:171 , LEU A:175BINDING SITE FOR RESIDUE IOD A 304
04AC4SOFTWAREHIS A:201BINDING SITE FOR RESIDUE IOD A 305
05AC5SOFTWAREASN B:133BINDING SITE FOR RESIDUE IOD B 302
06AC6SOFTWAREASN B:11 , ARG B:78BINDING SITE FOR RESIDUE IOD B 303
07AC7SOFTWAREALA B:171BINDING SITE FOR RESIDUE IOD B 304
08AC8SOFTWAREVAL B:105BINDING SITE FOR RESIDUE IOD B 305
09AC9SOFTWAREHIS B:201BINDING SITE FOR RESIDUE IOD B 306
10BC1SOFTWAREHIS B:37BINDING SITE FOR RESIDUE IOD B 307

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IK0)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val A:128 -Pro A:129
2Val B:128 -Pro B:129

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IK0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IK0)

(-) Exons   (0, 0)

(no "Exon" information available for 4IK0)

(-) 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
                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4ik0a1 A:1-130 Diaminopimelate epimerase                                                                                         d4ik0a2 A:131-274 Diaminopimelate epimerase                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeeee........hhhhhhhhhh........eeeeee........eeeeeee....ee.....hhhhhhhhhhhh......eeeeee..eeeeeee.....eeee......hhhhh..........eeeee..eeeeeeeee...eeeeeee......hhhhhhhhhhh........eeeeeeeee..eeeeeeee...eee..hhhhhhhhhhhhhhh.....eeeeee..eeeeeee......eeeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ik0 A   1 MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHYRIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGEPNFEPSAVPFRANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVETLGPVLESHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAEEVRVELPGGRLDIAWKGPGHPLYMTGPAVHVADGFIHL 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    


Chain B from PDB  Type:PROTEIN  Length:275
                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4ik0b1 B:1-130 Diaminopimelate epimerase                                                                                         d4ik0b2 B:131-275 Diaminopimelate epimerase                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeeee........hhhhhhhhhh........eeeeee........eeeeeee....ee.....hhhhhhhhhhhh......eeeeee..eeeeeee.....eeee......hhhhh..........eeeee..eeeeeeeee...eeeeee..hhhhhhhhhhhhhhhh........eeeeeeeee..eeeeeeee...ee...hhhhhhhhhhhhhhh.....eeeeee..eeeeeee......eeeee..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ik0 B   1 MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHYRIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGEPNFEPSAVPFRANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVETLGPVLESHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAEEVRVELPGGRLDIAWKGPGHPLYMTGPAVHVADGFIHLH 275
                                    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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4IK0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IK0)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/Swiss-Prot
        DAPF_ECOLI | P0A6K1: 4ijz

(-) Related Entries Specified in the PDB File

4ijz