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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) - 29 Jul 15  (Release) - 24 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
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, 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 BL21DE3/PET28B
    Gene: LDTB, RV2518C, RVBD_2518C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV
    Synonym: PROBABLE L,D-TRANSPEPTIDASE LDTB

 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  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1DWZ1Ligand/Ion(2S,3R,4S)-4-{[(3S,5S)-5-(DIMETHYLCARBAMOYL)PYRROLIDIN-3-YL]SULFANYL}-2-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-3-METHYL-3,4-DIHYDRO-2H-PYRROLE-5-CARBOXYLIC ACID
2MLD1Ligand/IonGLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1DWZ1Ligand/Ion(2S,3R,4S)-4-{[(3S,5S)-5-(DIMETHYLCARBAMOYL)PYRROLIDIN-3-YL]SULFANYL}-2-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-3-METHYL-3,4-DIHYDRO-2H-PYRROLE-5-CARBOXYLIC ACID
2MLD1Ligand/IonGLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1DWZ2Ligand/Ion(2S,3R,4S)-4-{[(3S,5S)-5-(DIMETHYLCARBAMOYL)PYRROLIDIN-3-YL]SULFANYL}-2-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-3-METHYL-3,4-DIHYDRO-2H-PYRROLE-5-CARBOXYLIC ACID
2MLD2Ligand/IonGLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:62 , THR A:63 , ALA A:64 , SER A:65 , SER A:80 , ARG A:139 , GLN A:140 , TYR A:155 , HOH A:615 , HOH A:665BINDING SITE FOR RESIDUE MLD A 501
2AC2SOFTWAREMET A:303 , TYR A:308 , TYR A:318 , GLY A:332 , HIS A:352 , CYS A:354BINDING SITE FOR RESIDUE DWZ A 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QR7)

(-) 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 4QR7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QR7)

(-) Exons   (0, 0)

(no "Exon" information available for 4QR7)

(-) 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:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...............eeeee..eeeeeeee........eee.....eeee........eeeeeeeee....eeeeeeeee.....eee.eeee.....ee.....eeeee.....hhhhhhhheeeeee....eeeee....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
                 4qr7 A  59 VPKLTASVTDGAVGVTVDAPVSVTAADGVLAAVTMVNDNGRPVAGRLSPDGLRWSTTEQLGYNRRYTLNATALGLGGAATRQLTFQTSSPAHLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAK 407
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398
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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 4QR7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QR7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QR7)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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  4qr7
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  LDT2_MYCTU | I6Y9J2
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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 4qra 4qrb 4qtf 5d7h 5dc2 5dcc 5du7 5duj 5dvp 5dzj 5dzp 5e1g 5e1i 5k69 5lb1 5lbg

(-) Related Entries Specified in the PDB File

4qra 4qrb