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(-) Description

Title :  STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF A NON-FUNCTIONALLY REDUNDANT M. TUBERCULOSIS (3,3) L,D-TRANSPEPTIDASE, LDTMT5.
 
Authors :  L. Basta, A. Ghosh, Y. Pan, J. Jakoncic, E. Lloyd, G. Townsend, G. Lamich M. A. Bianchet
Date :  06 Apr 15  (Deposition) - 02 Sep 15  (Release) - 28 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Peptidoglycan, Cell Wall Biosynthesis, Carbapenems, Nitrocefin, Enzyme Kinetics, Enzyme Structure, Antibiotics, Cell Wall, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. A. Brammer Basta, A. Ghosh, Y. Pan, J. Jakoncic, E. P. Lloyd, C. A. Townsend, G. Lamichhane, M. A. Bianchet
Loss Of A Functionally And Structurally Distinct Ld-Transpeptidase, Ldtmt5, Compromises Cell Wall Integrity In Mycobacterium Tuberculosis.
J. Biol. Chem. V. 290 25670 2015
PubMed-ID: 26304120  |  Reference-DOI: 10.1074/JBC.M115.660753
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MYCOBACTERIUM TUBERCULOSIS (3,3)L,D-TRANSPEPTIDASE TYPE 5
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Gene: LPRQ, MRA_0490
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25177 / H37RA)
    Organism Taxid: 419947
    Strain: ATCC 25177 / H37RA

 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  (4, 4)

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
3PGE1Ligand/IonTRIETHYLENE GLYCOL
4PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (4, 4)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
3PGE1Ligand/IonTRIETHYLENE GLYCOL
4PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (4, 8)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
3PGE2Ligand/IonTRIETHYLENE GLYCOL
4PO42Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:147 , GLU A:268 , THR A:384 , HOH A:611binding site for residue PO4 A 501
2AC2SOFTWAREPRO A:122 , LEU A:123 , TYR A:239 , HOH A:601 , HOH A:748binding site for residue PEG A 502
3AC3SOFTWAREGLU A:309 , LYS A:310 , PHE A:314 , TYR A:315 , MET A:316 , TYR A:372binding site for residue PGE A 503
4AC4SOFTWAREASN A:100 , LYS A:104 , TYR A:129binding site for residue ACE A 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z7A)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Arg A:70 -Pro A:71
2Asp A:199 -Pro A:200
3Asp A:396 -Ile A:397
4Pro A:415 -Pro A:416

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z7A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z7A)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z7A)

(-) 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:356
                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee....eeee......eeeee.eeeeeeeeee....ee.eee.....eeee........eeeeeeeeee....eee..eeeee....eee.eee......ee.....eeeee.....hhhhhhh.eeeeee....eeeeee.......eeeeee........eeeeee.....eee..eee...eeeeeee...eeeeee....eeeeee..eeeeeee.......hhhhh...eeee...eeee...............eeeee......eeee...........eeehhhhhhhhhhhh....eeeee......hhhhh..hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z7a A  56 LAEKRPPPAPRLTFRPADSAADVVPIAPISVEVGDGWFQRVALTNSAGKVVAGAYSRDRTIYTITEPLGYDTTYTWSGSAVGHDGKAVPVAGKFTTVAPVKTINAGFQLADGQTVGIAAPVIIQFDSPISDKAAVERALTVTTDPPVEGGWAWLPDEAQGARVHWRPREYYPAGTTVDVDAKLYGLPFGDGAYGAQDMSLHFQIGRRQVVKAEVSSHRIQVVTDAGVIMDFPCSYGEADLARNVTRNGIHVVTEKYSDFYMSNPAAGYSHIHERWAVRISNNGEFIHANPMNSNVTNGCINLSTENAEQYYRSAVYGDPVEVTGSSIQLSYADGDIWDWAVDWDTWVSMSALPPPx 504
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345||     361       371       381       391       401       411    ||
                                                                                                                                                                                                                                                                                                                            346|                                                            416|
                                                                                                                                                                                                                                                                                                                             353                                                             504-ACE
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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 4Z7A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z7A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z7A)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)

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  4z7a
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 Related Entries

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(-) Related Entries Specified in the PDB File

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