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(-) Description

Title :  CRYSTAL STRCUTURE OF OXIDIZED DAPF FROM CORYNEBACTERIUM GLUTAMICUM
 
Authors :  H. -Y. Sagong, K. -J. Kim
Date :  15 Oct 16  (Deposition) - 09 Nov 16  (Release) - 09 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. -Y. Sagong, K. -J. Kim
To Be Published
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: PET30A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: DAPF, CGL1943, CG2129
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM (STRAIN ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
    Organism Taxid: 196627
    Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
    Synonym: DAP EPIMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:40 , ASP A:47 , GLU A:217 , THR A:218 , ARG A:219 , ARG B:41binding site for residue GOL A 301
2AC2SOFTWAREARG A:40 , ARG A:41 , HOH A:542 , HOH A:552 , ARG B:40 , ARG B:41binding site for residue SO4 A 302

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1B:83 -B:221

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5H2G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5H2G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H2G)

(-) Exons   (0, 0)

(no "Exon" information available for 5H2G)

(-) 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:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee..eeeeeee........hhhhhhhhhh........eeeeeee.hhh.........eeeeeee..........hhhhhhhhhhhhh......eeee......eeeeeeee...eeeeeee....eeeeeeeeee..eeeeeeeee...eeeeee....hhhhhhhh.....ee.........eeeee......eeeeeeee...ee...hhhhhhhhhhhhhhhh....eeeeeee..eeeeeeee..eeeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h2g A   1 MNLTIPFAKGHATENDFIIIPDEDARLDLTPEMVVTLCDRRAGIGADGILRVVKAADVEGSTVDPSLWFMDYRNADGSLAEMCGNGVRLFAHWLYSRGLVDNTSFDIGTRAGVRHVDILQADQHSAQVRVDMGIPDVTGLSTCDINGQVFAGLGVDMGNPHLACVVPGLSASALADMELRAPTFDQEFFPHGVNVEIVTELEDDAVSMRVWERGVGETRSCGTGTVAAACAALADAGLGEGTVKVCVPGGEVEVQIFDDGSTLTGPSAIIALGEVQIH 278
                                    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:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee..eeeeeee........hhhhhhhhhh........eeeeeee.hhh.........eeeeeee..........hhhhhhhhhhhhh......eeee......eeeeeeee...eeeeeee....eeeeeeeeee..eeeeeeeee...eeeeee....hhhhhhhh.....ee.........eeeee......eeeeeeee...eee..hhhhhhhhhhhhhhhh....eeeeeee..eeeeeeee..eeeeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h2g B   1 MNLTIPFAKGHATENDFIIIPDEDARLDLTPEMVVTLCDRRAGIGADGILRVVKAADVEGSTVDPSLWFMDYRNADGSLAEMCGNGVRLFAHWLYSRGLVDNTSFDIGTRAGVRHVDILQADQHSAQVRVDMGIPDVTGLSTCDINGQVFAGLGVDMGNPHLACVVPGLSASALADMELRAPTFDQEFFPHGVNVEIVTELEDDAVSMRVWERGVGETRSCGTGTVAAACAALADAGLGEGTVKVCVPGGEVEVQIFDDGSTLTGPSAIIALGEVQIHHH 280
                                    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       280
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 5H2G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H2G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H2G)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DAPF_CORGL | Q8NP73: 5h2y 5m47

(-) Related Entries Specified in the PDB File

5h2y