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(-) Description

Title :  CRYSTAL STRUCTURE OF HALOALKANE DEHALOGENASE RV2579 FROM MYCOBACTERIUM TUBERCULOSIS COMPLEXED WITH 1,3-PROPANDIOL
 
Authors :  P. A. Mazumdar, J. Hulecki, M. M. Cherney, C. R. Garen, M. N. G. James, Tb Structural Genomics Consortium (Tbsgc)
Date :  29 Nov 06  (Deposition) - 13 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Haloalkane Dehalogenase, Mycobacterium Tuberculosis, Rv2579, 1, 3- Propandiol, Alpha/Beta-Hydrolase Protein, Tb Structural Genomics Consortium, Tbsgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. A. Mazumdar, J. Hulecki, M. M. Cherney, C. R. Garen, M. N. G. James
Crystal Structure Of Haloalkane Dehalogenase Rv2579 From Mycobacterium Tuberculosis Complexed With 1, 3-Propandiol
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HALOALKANE DEHALOGENASE 3
    Chains: A
    EC Number: 3.8.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST-15
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DHAA
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1BR1Ligand/IonBROMIDE ION
2PDO1Ligand/Ion1,3-PROPANDIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:39 , TRP A:110 , PRO A:209BINDING SITE FOR RESIDUE BR A 301
2AC2SOFTWAREALA A:248 , HIS A:273 , HOH A:529 , HOH A:579BINDING SITE FOR RESIDUE PDO A 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O2I)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:39 -Pro A:40
2Ser A:74 -Pro A:75
3Glu A:217 -Pro A:218
4Glu A:245 -Pro A:246

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O2I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2O2I)

(-) Exons   (0, 0)

(no "Exon" information available for 2O2I)

(-) Sequences/Alignments

Asymmetric/Biological 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:293
 aligned with DHAA_MYCTO | P9WMR8 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:293
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293   
           DHAA_MYCTO     4 FGVEPYGQPKYLEIAGKRMAYIDEGKGDAIVFQHGNPTSSYLWRNIMPHLEGLGRLVACDLIGMGASDKLSPSGPDRYSYGEQRDFLFALWDALDLGDHVVLVLHDWGSALGFDWANQHRDRVQGIAFMEAIVTPMTWADWPPAVRGVFQGFRSPQGEPMALEHNIFVERVLPGAILRQLSDEEMNHYRRPFVNGGEDRRPTLSWPRNLPIDGEPAEVVALVNEYRSWLEETDMPKLFINAEPGAIITGRIRDYVRSWPNQTEITVPGVHFVQEDSPEEIGAAIAQFVRRLRS 296
               SCOP domains d2o2ia_ A: automated matches                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2o2iA00 A:4-296  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                 CATH domains
               Pfam domains -----------------------------Abhydrolase_6-2o2iA01 A:33-286                                                                                                                                                                                                                                ---------- Pfam domains
         Sec.struct. author .........eeeee..eeeeeeee....eeeee.....hhhhhh.hhhhhh...eeeee...................hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhh..hhhhhhhh.hhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhh....eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o2i A   4 FGVEPYGQPKYLEIAGKRMAYIDEGKGDAIVFQHGNPTSSYLWRNIMPHLEGLGRLVACDLIGMGASDKLSPSGPDRYSYGEQRDFLFALWDALDLGDHVVLVLHDWGSALGFDWANQHRDRVQGIAFMEAIVTPMTWADWPPAVRGVFQGFRSPQGEPMALEHNIFVERVLPGAILRQLSDEEMNHYRRPFVNGGEDRRPTLSWPRNLPIDGEPAEVVALVNEYRSWLEETDMPKLFINAEPGAIITGRIRDYVRSWPNQTEITVPGVHFVQEDSPEEIGAAIAQFVRRLRS 296
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293   


Chain A from PDB  Type:PROTEIN  Length:293
 aligned with DHAA_MYCTU | P9WMR9 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:293
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293   
           DHAA_MYCTU     4 FGVEPYGQPKYLEIAGKRMAYIDEGKGDAIVFQHGNPTSSYLWRNIMPHLEGLGRLVACDLIGMGASDKLSPSGPDRYSYGEQRDFLFALWDALDLGDHVVLVLHDWGSALGFDWANQHRDRVQGIAFMEAIVTPMTWADWPPAVRGVFQGFRSPQGEPMALEHNIFVERVLPGAILRQLSDEEMNHYRRPFVNGGEDRRPTLSWPRNLPIDGEPAEVVALVNEYRSWLEETDMPKLFINAEPGAIITGRIRDYVRSWPNQTEITVPGVHFVQEDSPEEIGAAIAQFVRRLRS 296
               SCOP domains d2o2ia_ A: automated matches                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2o2iA00 A:4-296  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                 CATH domains
               Pfam domains -----------------------------Abhydrolase_6-2o2iA01 A:33-286                                                                                                                                                                                                                                ---------- Pfam domains
         Sec.struct. author .........eeeee..eeeeeeee....eeeee.....hhhhhh.hhhhhh...eeeee...................hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhh..hhhhhhhh.hhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhh....eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o2i A   4 FGVEPYGQPKYLEIAGKRMAYIDEGKGDAIVFQHGNPTSSYLWRNIMPHLEGLGRLVACDLIGMGASDKLSPSGPDRYSYGEQRDFLFALWDALDLGDHVVLVLHDWGSALGFDWANQHRDRVQGIAFMEAIVTPMTWADWPPAVRGVFQGFRSPQGEPMALEHNIFVERVLPGAILRQLSDEEMNHYRRPFVNGGEDRRPTLSWPRNLPIDGEPAEVVALVNEYRSWLEETDMPKLFINAEPGAIITGRIRDYVRSWPNQTEITVPGVHFVQEDSPEEIGAAIAQFVRRLRS 296
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: AB_hydrolase (347)

(-) Gene Ontology  (6, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DHAA_MYCTU | P9WMR9)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0018786    haloalkane dehalogenase activity    Catalysis of the reaction: 1-haloalkane + H2O = a primary alcohol + halide.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
    GO:0042206    halogenated hydrocarbon catabolic process    The chemical reactions and pathways resulting in the breakdown of halogenated hydrocarbons, any hydrocarbon with one or more halogen atoms attached to it.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A   (DHAA_MYCTO | P9WMR8)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0018786    haloalkane dehalogenase activity    Catalysis of the reaction: 1-haloalkane + H2O = a primary alcohol + halide.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DHAA_MYCTO | P9WMR8: 2o2h 2qvb
        DHAA_MYCTU | P9WMR9: 2o2h 2qvb

(-) Related Entries Specified in the PDB File

2o2h