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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS L,D-TRANSPEPTIDASE-2 (LDTMT2) BC-MODULE WITH THIONITROBENZOATE (TNB) ADDUCT AT THE ACTIVE SITE CYSTEINE-354
 
Authors :  E. M. Steiner, R. Schnell, G. Schneider
Date :  15 Jun 16  (Deposition) - 18 Jan 17  (Release) - 15 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cell Wall, Peptidoglycan, Transpeptidase, Mycobacterium Tuberculosis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. M. Steiner, G. Schneider, R. Schnell
Binding And Processing Of Beta-Lactam Antibiotics By The Transpeptidase Ldtmt2 From Mycobacterium Tuberculosis.
Febs J. V. 284 725 2017
PubMed-ID: 28075068  |  Reference-DOI: 10.1111/FEBS.14010

(-) Compounds

Molecule 1 - L,D-TRANSPEPTIDASE 2
    Chains: A, B
    EC Number: 2.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PNIC28BSA4
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 149-408
    Gene: LDTB, LPPS, RV2518C, RVBD_2518C, P425_02624
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Other Details: COVALENT ADDUCT (THIO-NITRO-BENZOATE) ON CYS354, MIXED DISULPHIDE BOND
    Strain: ATCC 25618 / H37RV
    Synonym: LDT 2,LDT(MT2)

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MNB2Ligand/Ion5-MERCAPTO-2-NITRO-BENZOIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MNB1Ligand/Ion5-MERCAPTO-2-NITRO-BENZOIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MNB1Ligand/Ion5-MERCAPTO-2-NITRO-BENZOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:308 , TYR A:318 , THR A:320 , HIS A:336 , TRP A:340 , CYS A:354 , HOH A:694 , HOH A:709 , HOH A:744 , HOH A:788binding site for residue MNB A 501
2AC2SOFTWARESER B:279 , MET B:280 , ASP B:304 , TYR B:308 , TYR B:318 , THR B:320 , GLY B:332 , PHE B:334 , HIS B:336 , SER B:351 , HIS B:352 , GLY B:353 , LEU B:355 , ASN B:356 , HOH B:790binding site for Di-peptide MNB B 501 and CYS B 354

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LB1)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Met A:157 -Pro A:158
2Asn A:193 -Pro A:194
3Met B:157 -Pro B:158
4Asn B:193 -Pro B:194

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LB1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LB1)

(-) Exons   (0, 0)

(no "Exon" information available for 5LB1)

(-) 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:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee.eeee.....ee.....eeeee.....hhhhhhhheeeeee....eeeee....eeeeee........eeeeee...........ee...eeeeeee...eeeeee....eeeeee..eeeeeee............eeee...eeeeeeee.hhhh.........eeeeeeeee......eeee.hhhh............eeehhhhhhhhhhhh....eeeee.............hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5lb1 A 150 HLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAK 407
                                   159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399        


Chain B from PDB  Type:PROTEIN  Length:253
                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.eeee.....ee.....eeeee.....hhhhhhhheeeeee....eeeee....eeeeee........eeeeee...........ee...eeeeeee...eeeeee....eeeeee..eeeeeee............eeee...eeeeeeee.hhh..eeeeeeeee......eeee.hhhh............eeehhhhhhhhhhhh....eeeee.............hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lb1 B 147 SMAHLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTYGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAK 407
                                   156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306 ||    324       334       344       354       364       374       384       394       404   
                                                                                                                                                                                           308|                                                                                          
                                                                                                                                                                                            317
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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 5LB1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LB1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LB1)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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  5lb1
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 Related Entries

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

UniProtKB/Swiss-Prot
        LDT2_MYCTU | I6Y9J2: 3vyn 3vyo 3vyp 4gsq 4gsr 4gsu 4hu2 4huc 4qr7 4qra 4qrb 4qtf 5d7h 5dc2 5dcc 5du7 5duj 5dvp 5dzj 5dzp 5e1g 5e1i 5k69 5lbg

(-) Related Entries Specified in the PDB File

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