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(-) Description

Title :  STRUCTURE AND SPECIFICITY OF L-D-TRANSPEPTIDASE FROM MYCOBACTERIUM TUBERCULOSIS AND ANTIBIOTIC RESISTANCE: CALCIUM BINDING PROMOTES DIMER FORMATION
 
Authors :  K. Gokulan, K. I. Varughese
Date :  30 Jun 14  (Deposition) - 23 Dec 15  (Release) - 24 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Structural Genomics, Enzyme Function Initiative, Center For Structural Genomics Of Infectious Diseases, Csgid, L-D- Transpeptidase; D-D-Transpeptidase; Single Anomalous Diffraction; Imipenem; Meropenem; Peptidoglycan; Beta-Lactamase, Peptide Cross Linkage, Peptidoglycan Stems, Bacterial Cell Wall Periplasmic Region, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Gokulan, S. Khare, C. E. Cerniglia, S. L. Foley, K. I. Varughese
Structure And Specificity Of L-D-Transpeptidase From Mycobacterium Tuberculosis And Antibiotic Resistance: Calcium Binding Promotes Dimer Formation
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - L,D-TRANSPEPTIDASE LDTB
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21DE3
    Expression System Taxid: 562
    Expression System Vector Type: E. COLI PET28B
    Gene: LDTB, RV2518C, RVBD_2518C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1MLD1Ligand/IonGLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MLD1Ligand/IonGLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MLD2Ligand/IonGLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:62 , THR A:63 , ALA A:64 , SER A:65 , SER A:80 , ARG A:139 , GLN A:140 , HOH A:662 , HOH A:808BINDING SITE FOR RESIDUE MLD A 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QRB)

(-) 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    
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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:339
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...............eeeee..eeeeeeee........eee.....eeee........eeeeeeeeee..eeeeeeeeee.....eee.eeee.....ee.....eeeee.....hhhhhhhheeeeee....eeeeeee..eeeeee........eeeeee..........eee...eeeeeee...eeeeee....eeeeee..eeeeeee............eeee...eeeee........eeeeee......eeee.hhhh............eeehhhhhhhhhhhh....eeeee.............hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qrb A  57 LLVPKLTASVTDGAVGVTVDAPVSVTAADGVLAAVTMVNDNGRPVAGRLSPDGLRWSTTEQLGYNRRYTLNATALGLGGAATRQLTFQTSSPAHLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAK 407
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306||     328       338       348       358       368       378       388       398         
                                                                                                                                                                                                                                                                                    307|                                                                                       
                                                                                                                                                                                                                                                                                     320
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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 4QRB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        LDT2_MYCTU | I6Y9J2: 3vyn 3vyo 3vyp 4gsq 4gsr 4gsu 4hu2 4huc 4qr7 4qra 4qtf 5d7h 5dc2 5dcc 5du7 5duj 5dvp 5dzj 5dzp 5e1g 5e1i 5k69 5lb1 5lbg

(-) Related Entries Specified in the PDB File

4qr7 4qra