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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 :  2.29
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
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; , 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, B
    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

 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, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:151 , HOH A:624 , HOH A:625 , LEU B:151 , HOH B:525 , HOH B:526 , HOH B:527BINDING SITE FOR RESIDUE CA A 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ala A:84 -Asp A:85
2Ala A:89 -Ala A:90
3Asn A:97 -Gly A:98
4Pro A:107 -Asp A:108
5Met A:157 -Pro A:158
6Asn A:193 -Pro A:194
7Gly B:86 -Val B:87
8Asp B:96 -Asn B:97
9Met B:157 -Pro B:158
10Asn B:193 -Pro B:194

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QRA)

(-) 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:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eee...........ee...............eee.........eee.....eee.....eee.eeee.....ee.....eeeee.....hhhhhhhheeeeee....eeeee....eeeeee........eeeeee..........eee...eeeeeee...eeeeee....eeeeee..eeeeeee............eeee...eeeeeeee.hhhh.........eeeeeeeee......eeee.hhhh............eeehhhhhhhhhhhh....eeeee.............hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qra A  64 ASVTDGAVGVTVDAPVSVTAADGVLAAVTMVNDNGRPVAGRLSPDGLRWSTTEQLGYNRRYTLTRQLTFQTSSPAHLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAKA 408
                                    73        83        93       103       113       123  ||   144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404    
                                                                                        126|                                                                                                                                                                                                                                                                              
                                                                                         138                                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:330
                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............eee.....................ee.....eeee........ee....ee.....eee.eeee.....ee.....eeeee.....hhhhhhhheeeeee....eeeee....eeeeee........eeeeee..........eee...eeeeeee...eeeeee....eeeeee..eeeeeee............eeee...eeeeeeee.hhhh.........eeeeeeeee......eeee.hhhh............eeehhhhhhhhhhhh....eeeee.............hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qra B  65 SVTDGAVGVTVDAPVSVTAADGVLAAVTMVNDNGRPVAGRLSPDGLRWSTTEQLGYNRRYTLLTFQTSSPAHLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAKA 408
                                    74        84        94       104       114       124 ||    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       408
                                                                                       126|                                                                                                                                                                                                                                                                           
                                                                                        141
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  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 4QRA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
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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 4qrb 4qtf 5d7h 5dc2 5dcc 5du7 5duj 5dvp 5dzj 5dzp 5e1g 5e1i 5k69 5lb1 5lbg

(-) Related Entries Specified in the PDB File

4qr7 4qrb