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(-) Description

Title :  CRYSTAL STRUCTURE OF LDTMT2, A L,D-TRANSPEPTIDASE FROM MYCOBACTERIUM TUBERCULOSIS: DOMAIN B AND C
 
Authors :  D. Both, E. Steiner, Y. Lindqvist, R. Schnell, G. Schneider
Date :  02 Nov 12  (Deposition) - 12 Dec 12  (Release) - 15 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Extracellular, Transpeptidase, Peptidoglycan Remodeling, Periplasmic, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Both, E. M. Steiner, D. Stadler, Y. Lindqvist, R. Schnell, G. Schneider
Structure Of Ldtmt2, An L, D-Transpeptidase From Mycobacterium Tuberculosis.
Acta Crystallogr. , Sect. D V. 69 432 2013
PubMed-ID: 23519418  |  Reference-DOI: 10.1107/S0907444912049268

(-) Compounds

Molecule 1 - PROBABLE CONSERVED LIPOPROTEIN LPPS
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28BSA4
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 149-408
    Gene: LPPS, MT2594, RV2518C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    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  (2, 14)

Asymmetric Unit (2, 14)
No.NameCountTypeFull Name
1ACT12Ligand/IonACETATE ION
2NA2Ligand/IonSODIUM ION
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1ACT8Ligand/IonACETATE ION
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2NA-1Ligand/IonSODIUM ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:310 , ASN A:316 , HOH A:608 , HOH A:834 , ASN B:313 , SER B:314 , PRO B:315 , HOH B:670BINDING SITE FOR RESIDUE ACT A 501
02AC2SOFTWAREASN A:204 , TYR A:330 , HOH A:813BINDING SITE FOR RESIDUE ACT A 502
03AC3SOFTWAREMET A:303 , TYR A:318 , THR A:320 , HIS A:352 , HOH A:812 , HOH A:814 , HOH A:827BINDING SITE FOR RESIDUE ACT A 503
04AC4SOFTWARELYS A:299 , ASP A:323 , TRP A:324 , HOH A:763BINDING SITE FOR RESIDUE ACT A 504
05AC5SOFTWAREASP A:223 , HIS A:246 , ARG A:319 , GLY B:343 , ALA B:344 , HIS B:347 , THR B:348BINDING SITE FOR RESIDUE ACT A 505
06AC6SOFTWAREHIS A:214 , PHE A:215 , ACT A:508 , HOH A:803BINDING SITE FOR RESIDUE ACT A 506
07AC7SOFTWARELEU A:385 , PRO A:386 , GLY A:387 , ASN A:395 , HOH A:694BINDING SITE FOR RESIDUE ACT A 507
08AC8SOFTWAREILE A:291 , GLU A:376 , ACT A:506 , HOH A:835BINDING SITE FOR RESIDUE ACT A 508
09AC9SOFTWAREVAL A:342 , GLY A:343 , GLN A:345 , HOH A:653 , HOH A:713 , HOH A:774BINDING SITE FOR RESIDUE NA A 509
10BC1SOFTWAREILE B:188 , LYS B:189 , ILE B:190 , HOH B:645 , HOH B:743BINDING SITE FOR RESIDUE ACT B 501
11BC2SOFTWAREMET B:303 , TYR B:318 , THR B:320 , HIS B:352 , HOH B:789 , HOH B:793 , HOH B:799BINDING SITE FOR RESIDUE ACT B 502
12BC3SOFTWAREHIS B:214 , PHE B:215 , HOH B:762BINDING SITE FOR RESIDUE ACT B 503
13BC4SOFTWAREASP B:160 , GLN B:244 , HOH B:646BINDING SITE FOR RESIDUE ACT B 504
14BC5SOFTWAREHOH A:709 , VAL B:342 , GLY B:343 , GLN B:345 , HOH B:633 , HOH B:754BINDING SITE FOR RESIDUE NA B 505

(-) SS Bonds  (0, 0)

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

(-) 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 4HUC)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HUC)

(-) 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:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.eeee.....ee.....eeeee.....hhhhhhhheeeeee....eeeeeee..eeeeee........eeeeeee.........eee..eeeeeeee...eeeeee....eeeeee..eeeeeee............eeee...eeeeeeee.hhhh.........eeeeeeeee......eeee.hhhh............eeehhhhhhhhhhhh....eeeee.............hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4huc A 148 MAHLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAKA 408
                                   157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407 


Chain B from PDB  Type:PROTEIN  Length:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .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
                 4huc B 149 AHLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAKA 408
                                   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
   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 4HUC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 22)

Asymmetric Unit(hide GO term definitions)

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    Asn A:193 - Pro A:194   [ RasMol ]  
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 Related Entries

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        LDT2_MYCTO | O53223: 3tur 3tx4 3u1p 3u1q 3vae 3vyn 3vyo 3vyp 4gsq 4gsr 4gsu 4hu2 5d7h 5dc2 5dcc 5du7 5duj 5lbg
        LDT2_MYCTU | I6Y9J2: 3vyn 3vyo 3vyp 4gsq 4gsr 4gsu 4hu2 4qr7 4qra 4qrb 4qtf 5d7h 5dc2 5dcc 5du7 5duj 5dvp 5dzj 5dzp 5e1g 5e1i 5k69 5lb1 5lbg

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4hu2