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(-) Description

Title :  CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH ALPHA-KETOPIMELIC ACID
 
Authors :  V. Navratna, B. Gopal
Date :  02 Apr 16  (Deposition) - 17 Aug 16  (Release) - 17 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Dap Pathway, L-Lysine, Alpha-Ketopimelic Acid, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Shrivastava, V. Navratna, Y. Silla, R. P. Dewangan, A. Pramanik, S. Chaudhary, G. Rayasam, A. Kumar, B. Gopal, S. Ramachandran
Inhibition Of Mycobacterium Tuberculosis Dihydrodipicolinat Synthase By Alpha-Ketopimelic Acid And Its Other Structural Analogues
Sci Rep V. 6 30827 2016
PubMed: search  |  Reference-DOI: DOI:10.1038/SREP30827

(-) Compounds

Molecule 1 - 4-HYDROXY-TETRAHYDRODIPICOLINATE SYNTHASE
    Chains: A
    EC Number: 4.3.3.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DAPA
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS H37RV
    Organism Taxid: 83332
    Strain: H37RV
    Synonym: DIHYDRODIPICOLINATE SYNTHASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
16GT1Ligand/Ion2-OXOHEPTANEDIOIC ACID
2NA2Ligand/IonSODIUM ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
16GT4Ligand/Ion2-OXOHEPTANEDIOIC ACID
2NA-1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:152 , GLU A:154 , PRO A:155 , LYS A:174binding site for residue NA A 401
2AC2SOFTWAREGLU A:154 , ASP A:156binding site for residue NA A 402
3AC3SOFTWAREALA A:18 , THR A:54 , THR A:55 , TYR A:143 , ILE A:145 , ARG A:148 , LYS A:171 , GLY A:194 , VAL A:213 , HOH A:530 , HOH A:578binding site for residue 6GT A 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5J5D)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:4 -Gly A:5
2Leu A:276 -Pro A:277

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5J5D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J5D)

(-) Exons   (0, 0)

(no "Exon" information available for 5J5D)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  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:297
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..eeee...........hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhh...eeeeee...hhhhhhhhhhhhh.eeee.hhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j5d A   4 VGFDVAARLGTLLTAMVTPFSGDGSLDTATAARLANHLVDQGCDGLVVSGTTGESPTTTDGEKIELLRAVLEAVGDRARVIAGAGTYDTAHSIRLAKACAAEGAHGLLVVTPYYSKPPQRGLQAHFTAVADATELPMLLYDIPGRSAVPIEPDTIRALASHPNIVGVKDAKADLHSGAQIMADTGLAYYSGDDALNLPWLAMGATGFISVIAHLAAGQLRELLSAFGSGDIATARKINIAVAPLCNAMSRLGGVTLSKAGLRLQGIDVGDPRLPQVAATPEQIDALAADMRAASVLR 300
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293
   Legend:   → Mismatch (orange background)
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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 5J5D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J5D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J5D)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        DAPA_MYCTU | P9WP25: 1xxx 3l21

(-) Related Entries Specified in the PDB File

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