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(-) Description

Title :  CRYSTAL STRCUTURE OF DAPD FROM CORYNEBACTERIUM GLUTAMICUM
 
Authors :  H. -Y. Sagong, K. -J. Kim
Date :  03 Oct 15  (Deposition) - 04 Nov 15  (Release) - 30 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Transferase, Corynebacterium Glutamicum, L-Lysine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Y. Sagong, K. J. Kim
Crystal Structure And Biochemical Characterization Of Tetrahydrodipicolinate N-Succinyltransferase From Corynebacterium Glutamicum.
J. Agric. Food Chem. V. 63 10641 2015
PubMed-ID: 26602189  |  Reference-DOI: 10.1021/ACS.JAFC.5B04785

(-) Compounds

Molecule 1 - 2,3,4,5-TETRAHYDROPYRIDINE-2,6-DICARBOXYLATE N- SUCCINYLTRANSFERASE
    Chains: A
    EC Number: 2.3.1.117
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: DAPD, CGL1106, CG1256
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM
    Organism Taxid: 196627
    Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
    Synonym: TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE,THP SUCCINYLTRANSFERASE,TETRAHYDROPICOLINATE SUCCINYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1PG41Ligand/IonTETRAETHYLENE GLYCOL
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1PG43Ligand/IonTETRAETHYLENE GLYCOL
2SO43Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:241 , LEU A:242 , LYS A:249 , ARG A:272 , SER A:274 , GLY A:277 , HOH A:507 , HOH A:508 , HOH A:552binding site for residue PG4 A 401
2AC2SOFTWAREVAL A:106 , GLY A:108 , PHE A:109 , ALA A:110 , LYS A:218 , ARG A:219binding site for residue SO4 A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5E3P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5E3P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E3P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E3P)

(-) Exons   (0, 0)

(no "Exon" information available for 5E3P)

(-) 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:284
                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee....eeeee...........hhhhheee....eeeeeeeeeee......hhhhhhhhhhhhhh...........hhhhh...eeee..eeee..hhhhhhhhhh......eeeee...hhhhh......ee.hhhhh....ee....ee....ee....ee....ee..ee....ee....ee....ee............ee....ee....ee........ee....ee....eeee..eeee.hhhh....eeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e3p A   2 TTASATGIATLTSTGDVLDVWYPEIGSTDQSALTPLEGVDEDRNVTRKIVTTTIDIDAAPTDTYDAWLRLHLLSHRVFRPHTINLDGIFGLLNNVVWTNFGPCAVDGFALTRARLSRRGQVTVYSVDKFPRMVDYVVPSGVRIGDADRVRLGAYLADGTTVMHEGFVNFNAGTLGASMVEGRISAGVTVDDGTDVGGGASIMGTLSGGGQHVISLGKRCLLGANSGCGIPLGDDCIIEAGLYITAGTKVLFDGSLHKASTLAGSNGLIFRRDSVSGQVVAVPNT 285
                                    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
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  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 5E3P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E3P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E3P)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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  5e3p
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  2.3.1.117
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 Related Entries

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

UniProtKB/Swiss-Prot
        DAPD_CORGL | Q8NRE3: 5e3q 5e3r

(-) Related Entries Specified in the PDB File

5e3q 5e3r