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(-) Description

Title :  ASYMMETRY IN THE ACTIVE SITE OF MYCOBACTERIUM TUBERCULOSIS AHPE UPON EXPOSURE TO MYCOTHIOL
 
Authors :  A. Kumar, A. M. Balakrishna, G. Gruber
Date :  23 Feb 16  (Deposition) - 03 Aug 16  (Release) - 24 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.43
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Thioredoxin Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kumar, A. M. Balakrishna, W. Nartey, M. S. S. Manimekalai, G. Gruber
Redox Chemistry Of Mycobacterium Tuberculosis Alkylhydroperoxide Reductase E (Ahpe): Structural And Mechanistic Insight Into A Mycoredoxin-1 Independent Reductive Pathway Of Ahpe Via Mycothiol
Free Radic. Biol. Med. V. 97 588 2016
PubMed-ID: 27417938  |  Reference-DOI: 10.1016/J.FREERADBIOMED.2016.07.007
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE PEROXIREDOXIN RV2238C
    Atcc: ATCC 25618
    Chains: A, D
    EC Number: 1.11.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET9D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RV2238C, MTAHPE
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS H37RV
    Organism Taxid: 83332
    Strain: H37RV
    Synonym: THIOREDOXIN REDUCTASE
 
Molecule 2 - PUTATIVE PEROXIREDOXIN RV2238C
    Atcc: ATCC 25618
    Chains: B, C
    EC Number: 1.11.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET9D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RV2238C, MTAHPE
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS H37RV
    Organism Taxid: 83332
    Strain: H37RV
    Synonym: THIOREDOXIN REDUCTASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CSO2Mod. Amino AcidS-HYDROXYCYSTEINE
3GOL2Ligand/IonGLYCEROL
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
3GOL2Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
3GOL-1Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:13 , ARG A:14 , SER A:92 , PHE A:94 , TRP A:95 , PRO A:96 , HOH A:311 , HOH A:342binding site for residue GOL A 201
2AC2SOFTWARETHR B:87 , HOH B:307binding site for residue ACT B 201
3AC3SOFTWAREASN B:17 , GLN B:19 , ASN B:108 , GLN B:110 , ASN B:115 , GLN B:134 , HOH B:322 , HOH B:348binding site for residue GOL B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5ID2)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Trp A:95 -Pro A:96
2Trp B:95 -Pro B:96
3Trp C:95 -Pro C:96
4Trp D:95 -Pro D:96

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5ID2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5ID2)

(-) Exons   (0, 0)

(no "Exon" information available for 5ID2)

(-) 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:154
                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee.....eee.hhhh...eeeeee.....hhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhh....eee.....hhhhhhh..ee....ee.eeeeee.....eeeeeee......hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5id2 A   0 VMLNVGATAPDFTLRDQNQQLVTLRGYRGAKNVLLVFFPLAFTGIcQGELDQLRDHLPEFENDDSAALAISVGPPPTHKIWATQSGFTFPLLSDFWPHGAVSQAYGVFNEQAGIANRGTFVVDRSGIIRFAEMKQPGEVRDQRLWTDALAALTA 153
                                     9        19        29        39     |  49        59        69        79        89        99       109       119       129       139       149    
                                                                        45-CSO                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eee.....eee.hhhh...eeeeee.....hhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhh....eee.....hhhhhhh..ee....ee.eeeeee.....eeeeeee......hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5id2 B  -3 HPMVMLNVGATAPDFTLRDQNQQLVTLRGYRGAKNVLLVFFPLAFTGICQGELDQLRDHLPEFENDDSAALAISVGPPPTHKIWATQSGFTFPLLSDFWPHGAVSQAYGVFNEQAGIANRGTFVVDRSGIIRFAEMKQPGEVRDQRLWTDALAALTA 153
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       


Chain C from PDB  Type:PROTEIN  Length:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eee.....eee.hhhh...eeeeee.....hhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhh....eee.....hhhhhhh..ee....ee.eeeeee.....eeeeeee......hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5id2 C  -3 HPMVMLNVGATAPDFTLRDQNQQLVTLRGYRGAKNVLLVFFPLAFTGICQGELDQLRDHLPEFENDDSAALAISVGPPPTHKIWATQSGFTFPLLSDFWPHGAVSQAYGVFNEQAGIANRGTFVVDRSGIIRFAEMKQPGEVRDQRLWTDALAALTA 153
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       


Chain D from PDB  Type:PROTEIN  Length:155
                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eee.....eee.hhhh...eeeeee.....hhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhh....eee.....hhhhhhh..ee....ee..eeeee.....eeeeee.......hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5id2 D  -1 MVMLNVGATAPDFTLRDQNQQLVTLRGYRGAKNVLLVFFPLAFTGIcQGELDQLRDHLPEFENDDSAALAISVGPPPTHKIWATQSGFTFPLLSDFWPHGAVSQAYGVFNEQAGIANRGTFVVDRSGIIRFAEMKQPGEVRDQRLWTDALAALTA 153
                                     8        18        28        38      | 48        58        68        78        88        98       108       118       128       138       148     
                                                                         45-CSO
   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 5ID2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5ID2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5ID2)

(-) Gene Ontology  (10, 10)

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        Y2238_MYCTU | P9WIE3: 1xvw 1xxu 4x0x 4x1u 4xih 5c04

(-) Related Entries Specified in the PDB File

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