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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF A ENZYMATICALLY DEGRADED BIAPENEM-ADDUCT OF L,D-TRANSPEPTIDASE 2 FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  Y. Pan, L. Basta, G. Lamichhane, M. A. Bianchet
Date :  23 Aug 15  (Deposition) - 05 Oct 16  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.18
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  L, D-Transpeptidase, Carbapenems Biapenem-Adduct, Ldtmt2, Mycobacterium Tuberculosis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Bianchet, Y. H. Pan, L. A. B. Basta, H. Saavedra, E. P. Lloyd, P. Kumar, R. Mattoo, C. A. Townsend, G. Lamichhane
Structural Insight Into The Inactivation Of Mycobacterium Tuberculosis Non-Classical Transpeptidase Ldtmt2 By Biapene And Tebipenem.
Bmc Biochem. V. 18 8 2017
PubMed-ID: 28545389  |  Reference-DOI: 10.1186/S12858-017-0082-4
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - L,D-TRANSPEPTIDASE 2
    Chains: A, B
    EC Number: 2.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 56-408
    Gene: LDTB, MT2594, V735_02606
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS (STRAIN CDC 1551 / OSHKOSH)
    Organism Taxid: 83331
    Strain: CDC 1551 / OSHKOSH
    Synonym: LDT 2,LDT(MT2)

 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  (6, 33)

Asymmetric Unit (6, 33)
No.NameCountTypeFull Name
158U2Ligand/Ion(4S)-4-METHYL-2,5,7-TRIOXOHEPTANOIC ACID
2EDO2Ligand/Ion1,2-ETHANEDIOL
3GOL5Ligand/IonGLYCEROL
4PEG9Ligand/IonDI(HYDROXYETHYL)ETHER
5PGE5Ligand/IonTRIETHYLENE GLYCOL
6SO410Ligand/IonSULFATE ION
Biological Unit 1 (6, 16)
No.NameCountTypeFull Name
158U1Ligand/Ion(4S)-4-METHYL-2,5,7-TRIOXOHEPTANOIC ACID
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GOL3Ligand/IonGLYCEROL
4PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
5PGE2Ligand/IonTRIETHYLENE GLYCOL
6SO45Ligand/IonSULFATE ION
Biological Unit 2 (6, 17)
No.NameCountTypeFull Name
158U1Ligand/Ion(4S)-4-METHYL-2,5,7-TRIOXOHEPTANOIC ACID
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GOL2Ligand/IonGLYCEROL
4PEG5Ligand/IonDI(HYDROXYETHYL)ETHER
5PGE3Ligand/IonTRIETHYLENE GLYCOL
6SO45Ligand/IonSULFATE ION

(-) Sites  (33, 33)

Asymmetric Unit (33, 33)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET A:303 , TYR A:318 , GLY A:332 , HIS A:336 , TRP A:340 , SER A:351 , HIS A:352 , GLY A:353 , CYS A:354 , ASN A:356 , EDO A:516 , HOH A:606 , HOH A:625binding site for residue 58U A 501
02AC2SOFTWAREARG A:122 , SO4 A:506 , HOH A:601 , HOH A:656 , PRO B:311 , VAL B:312 , ASN B:313 , HOH B:641binding site for residue SO4 A 502
03AC3SOFTWAREARG A:371 , HOH A:626 , HOH A:652 , HOH A:695 , HOH A:758binding site for residue SO4 A 503
04AC4SOFTWAREMET A:157 , TYR A:330 , ARG A:371 , HOH A:605binding site for residue SO4 A 504
05AC5SOFTWARESER A:106 , PRO A:107 , ARG A:111 , HOH A:628 , HOH A:703binding site for residue SO4 A 505
06AC6SOFTWAREASN A:95 , ARG A:99 , SO4 A:502 , HOH A:601 , HOH A:619 , SER B:306binding site for residue SO4 A 506
07AC7SOFTWAREASN A:204 , ASN A:205 , HOH A:761binding site for residue PEG A 507
08AC8SOFTWAREGLY A:86 , LEU A:131 , GLY A:132 , HOH A:615binding site for residue PEG A 508
09AC9SOFTWAREGLU A:185 , ALA A:199 , PHE A:200 , TRP A:401 , ARG A:402 , GLY A:404 , PEG A:510 , HOH A:688binding site for residue PEG A 509
10AD1SOFTWAREILE A:188 , LYS A:189 , ILE A:190 , GLY A:198 , TRP A:210 , PEG A:509 , HOH A:750binding site for residue PEG A 510
11AD2SOFTWAREHIS A:214 , PHE A:215 , GLU A:252 , ILE A:254 , HOH A:638 , LYS B:186binding site for residue PGE A 511
12AD3SOFTWARELYS A:189 , ILE A:190 , THR A:192 , VAL A:196 , HOH A:719 , ASN B:260binding site for residue PGE A 512
13AD4SOFTWAREARG A:123 , THR A:142 , SER A:358 , PRO A:359 , SER A:360 , HOH A:603 , HOH A:714binding site for residue GOL A 513
14AD5SOFTWAREARG A:181 , TRP A:202 , LEU A:203 , HOH A:608 , HOH A:621binding site for residue GOL A 514
15AD6SOFTWAREVAL A:75 , ALA A:77 , PRO A:78 , GLN A:117 , LEU A:118 , HOH A:763binding site for residue GOL A 515
16AD7SOFTWARETYR A:318 , SER A:331 , HIS A:352 , GLY A:353 , 58U A:501binding site for residue EDO A 516
17AD8SOFTWAREARG B:297 , ARG B:371 , HOH B:621 , HOH B:681binding site for residue SO4 B 502
18AD9SOFTWAREPRO A:311 , VAL A:312 , ASN A:313 , ARG B:122 , SO4 B:504 , HOH B:616 , HOH B:623 , HOH B:749binding site for residue SO4 B 503
19AE1SOFTWARESER A:306 , PRO A:311 , ASN B:95 , ASN B:97 , ARG B:99 , SO4 B:503 , HOH B:658binding site for residue SO4 B 504
20AE2SOFTWAREARG B:104 , SER B:106 , PRO B:107 , ARG B:111 , HOH B:630 , HOH B:748binding site for residue SO4 B 505
21AE3SOFTWARELEU A:62 , ARG A:139 , LEU A:141 , ASP B:399 , HOH B:609 , HOH B:622binding site for residue PEG B 507
22AE4SOFTWAREILE B:190 , TRP B:210binding site for residue PEG B 508
23AE5SOFTWAREVAL A:71 , HOH A:843 , GLU B:213 , HIS B:214binding site for residue PEG B 509
24AE6SOFTWAREPRO B:386 , GLY B:387 , GLN B:400 , PGE B:514 , HOH B:610 , HOH B:613binding site for residue PEG B 510
25AE7SOFTWAREASP B:251 , HIS B:368 , HOH B:611 , HOH B:635binding site for residue PEG B 511
26AE8SOFTWAREGLU B:376 , VAL B:378 , PRO B:397 , GOL B:515 , HOH B:603 , HOH B:763binding site for residue PGE B 512
27AE9SOFTWAREGLU B:168 , PRO B:169 , ALA B:171 , GLY B:295 , SER B:296 , GLN B:327 , TYR B:330 , ARG B:371binding site for residue PGE B 513
28AF1SOFTWAREARG B:181 , TYR B:201 , TRP B:202 , ILE B:388 , ASN B:405 , ALA B:408 , PEG B:510 , HOH B:610binding site for residue PGE B 514
29AF2SOFTWAREGLU B:213 , HIS B:214 , PHE B:215 , ILE B:291 , PGE B:512 , HOH B:750binding site for residue GOL B 515
30AF3SOFTWAREALA B:90 , VAL B:91 , LEU B:105 , TRP B:112binding site for residue GOL B 516
31AF4SOFTWARETYR B:318 , SER B:331 , GLY B:332 , 58U B:501binding site for residue EDO B 517
32AF5SOFTWARESER B:279 , MET B:280 , MET B:303 , TYR B:318 , GLY B:332 , PHE B:334 , HIS B:336 , TRP B:340 , SER B:351 , HIS B:352 , GLY B:353 , LEU B:355 , ASN B:356 , EDO B:517 , HOH B:612binding site for Di-peptide 58U B 501 and CYS B 354
33AF6SOFTWAREASN B:95 , ASP B:96 , ARG B:122 , TYR B:124 , PHE B:143 , GLN B:144 , SER B:358 , SER B:360 , HOH B:605 , HOH B:638 , HOH B:732binding site for Di-peptide SO4 B 506 and ARG B 123

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DC2)

(-) 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 5DC2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DC2)

(-) Exons   (0, 0)

(no "Exon" information available for 5DC2)

(-) 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:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee...............eeeee..eeeeeeeee.......eee.....eeee........eeeeeeeeee..eeeeeeeeee.....eee.eeee.....ee.....eeeee.....hhhhhhhheeeeee....eeeee....eeeeee........eeeeee.....eee..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
                 5dc2 A  56 DLLVPKLTASVTDGAVGVTVDAPVSVTAADGVLAAVTMVNDNGRPVAGRLSPDGLRWSTTEQLGYNRRYTLNATALGLGGAATRQLTFQTSSPAHLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAK 407
                                    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       355       365       375       385       395       405  


Chain B from PDB  Type:PROTEIN  Length:353
                                                                                                                                                                                                                                                                                                                                                                                                 
               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....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
                 5dc2 B  56 DLLVPKLTASVTDGAVGVTVDAPVSVTAADGVLAAVTMVNDNGRPVAGRLSPDGLRWSTTEQLGYNRRYTLNATALGLGGAATRQLTFQTSSPAHLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAKA 408
                                    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       355       365       375       385       395       405
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 5DC2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DC2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DC2)

(-) Gene Ontology  (14, 22)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        LDT2_MYCTO | O53223: 3tur 3tx4 3u1p 3u1q 3vae 3vyn 3vyo 3vyp 4gsq 4gsr 4gsu 4hu2 4huc 5d7h 5dcc 5du7 5duj 5lbg
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(-) Related Entries Specified in the PDB File

3tur 5dcc