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(-) Description

Title :  CRYSTAL STRUCTURE OF HALOALKANE DEHALOGENASE RV2579 FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  P. A. Mazumdar, J. Hulecki, M. M. Cherney, C. R. Garen, M. N. G. James, Tb Structural Genomics Consortium (Tbsgc)
Date :  08 Aug 07  (Deposition) - 12 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.19
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rv2579, Haloalkane Dehalogenase, Alpha-Beta Hydrolase Protein, Tb Structural Genomics Consortium, Tbsgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. A. Mazumdar, J. C. Hulecki, M. M. Cherney, C. R. Garen, M. N. James
X-Ray Crystal Structure Of Mycobacterium Tuberculosis Haloalkane Dehalogenase Rv2579.
Biochim. Biophys. Acta V. 1784 351 2008
PubMed-ID: 18062934  |  Reference-DOI: 10.1016/J.BBAPAP.2007.10.014

(-) Compounds

Molecule 1 - HALOALKANE DEHALOGENASE 3
    Chains: A, B
    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

  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, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:39 , TRP A:110 , TRP A:208 , PRO A:209 , HOH A:632BINDING SITE FOR RESIDUE CL A 2
2AC2SOFTWAREASN B:39 , TRP B:110 , TRP B:208 , PRO B:209 , HOH B:629BINDING SITE FOR RESIDUE CL B 2
3AC3SOFTWAREVAL A:174 , HIS A:273 , HOH A:637BINDING SITE FOR RESIDUE EDO A 1
4AC4SOFTWAREHIS B:273 , HOH B:630BINDING SITE FOR RESIDUE EDO B 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric 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
5Asn B:39 -Pro B:40
6Ser B:74 -Pro B:75
7Glu B:217 -Pro B:218
8Glu B:245 -Pro B:246

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2QVB)

(-) 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:297
 aligned with DHAA_MYCTO | P9WMR8 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:297
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       
           DHAA_MYCTO     3 AFGVEPYGQPKYLEIAGKRMAYIDEGKGDAIVFQHGNPTSSYLWRNIMPHLEGLGRLVACDLIGMGASDKLSPSGPDRYSYGEQRDFLFALWDALDLGDHVVLVLHDWGSALGFDWANQHRDRVQGIAFMEAIVTPMTWADWPPAVRGVFQGFRSPQGEPMALEHNIFVERVLPGAILRQLSDEEMNHYRRPFVNGGEDRRPTLSWPRNLPIDGEPAEVVALVNEYRSWLEETDMPKLFINAEPGAIITGRIRDYVRSWPNQTEITVPGVHFVQEDSPEEIGAAIAQFVRRLRSAAG 299
               SCOP domains d2qvba_ A: automated matches                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2qvbA00 A:3-299  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee..eeeeeeee....eeeee.....hhhhhh.hhhhhh...eeeee...................hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhh..hhhhhhhh.hhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qvb A   3 AFGVEPYGQPKYLEIAGKRMAYIDEGKGDAIVFQHGNPTSSYLWRNIMPHLEGLGRLVACDLIGMGASDKLSPSGPDRYSYGEQRDFLFALWDALDLGDHVVLVLHDWGSALGFDWANQHRDRVQGIAFMEAIVTPMTWADWPPAVRGVFQGFRSPQGEPMALEHNIFVERVLPGAILRQLSDEEMNHYRRPFVNGGEDRRPTLSWPRNLPIDGEPAEVVALVNEYRSWLEETDMPKLFINAEPGAIITGRIRDYVRSWPNQTEITVPGVHFVQEDSPEEIGAAIAQFVRRLRSAAG 299
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       


Chain A from PDB  Type:PROTEIN  Length:297
 aligned with DHAA_MYCTU | P9WMR9 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:297
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       
           DHAA_MYCTU     3 AFGVEPYGQPKYLEIAGKRMAYIDEGKGDAIVFQHGNPTSSYLWRNIMPHLEGLGRLVACDLIGMGASDKLSPSGPDRYSYGEQRDFLFALWDALDLGDHVVLVLHDWGSALGFDWANQHRDRVQGIAFMEAIVTPMTWADWPPAVRGVFQGFRSPQGEPMALEHNIFVERVLPGAILRQLSDEEMNHYRRPFVNGGEDRRPTLSWPRNLPIDGEPAEVVALVNEYRSWLEETDMPKLFINAEPGAIITGRIRDYVRSWPNQTEITVPGVHFVQEDSPEEIGAAIAQFVRRLRSAAG 299
               SCOP domains d2qvba_ A: automated matches                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2qvbA00 A:3-299  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee..eeeeeeee....eeeee.....hhhhhh.hhhhhh...eeeee...................hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhh..hhhhhhhh.hhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qvb A   3 AFGVEPYGQPKYLEIAGKRMAYIDEGKGDAIVFQHGNPTSSYLWRNIMPHLEGLGRLVACDLIGMGASDKLSPSGPDRYSYGEQRDFLFALWDALDLGDHVVLVLHDWGSALGFDWANQHRDRVQGIAFMEAIVTPMTWADWPPAVRGVFQGFRSPQGEPMALEHNIFVERVLPGAILRQLSDEEMNHYRRPFVNGGEDRRPTLSWPRNLPIDGEPAEVVALVNEYRSWLEETDMPKLFINAEPGAIITGRIRDYVRSWPNQTEITVPGVHFVQEDSPEEIGAAIAQFVRRLRSAAG 299
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       


Chain B from PDB  Type:PROTEIN  Length:297
 aligned with DHAA_MYCTO | P9WMR8 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:297
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       
           DHAA_MYCTO     3 AFGVEPYGQPKYLEIAGKRMAYIDEGKGDAIVFQHGNPTSSYLWRNIMPHLEGLGRLVACDLIGMGASDKLSPSGPDRYSYGEQRDFLFALWDALDLGDHVVLVLHDWGSALGFDWANQHRDRVQGIAFMEAIVTPMTWADWPPAVRGVFQGFRSPQGEPMALEHNIFVERVLPGAILRQLSDEEMNHYRRPFVNGGEDRRPTLSWPRNLPIDGEPAEVVALVNEYRSWLEETDMPKLFINAEPGAIITGRIRDYVRSWPNQTEITVPGVHFVQEDSPEEIGAAIAQFVRRLRSAAG 299
               SCOP domains d2qvbb_ B: automated matches                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2qvbB00 B:3-299  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                     CATH domains
           Pfam domains (1) ------------------------------Abhydrolase_6-2qvbB01 B:33-286                                                                                                                                                                                                                                ------------- Pfam domains (1)
           Pfam domains (2) ------------------------------Abhydrolase_6-2qvbB02 B:33-286                                                                                                                                                                                                                                ------------- Pfam domains (2)
         Sec.struct. author ..........eeeee..eeeeeeee....eeeee.....hhhhhh.hhhhhh...eeeee...................hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhh..hhhhhhhh.hhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qvb B   3 AFGVEPYGQPKYLEIAGKRMAYIDEGKGDAIVFQHGNPTSSYLWRNIMPHLEGLGRLVACDLIGMGASDKLSPSGPDRYSYGEQRDFLFALWDALDLGDHVVLVLHDWGSALGFDWANQHRDRVQGIAFMEAIVTPMTWADWPPAVRGVFQGFRSPQGEPMALEHNIFVERVLPGAILRQLSDEEMNHYRRPFVNGGEDRRPTLSWPRNLPIDGEPAEVVALVNEYRSWLEETDMPKLFINAEPGAIITGRIRDYVRSWPNQTEITVPGVHFVQEDSPEEIGAAIAQFVRRLRSAAG 299
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       


Chain B from PDB  Type:PROTEIN  Length:297
 aligned with DHAA_MYCTU | P9WMR9 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:297
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       
           DHAA_MYCTU     3 AFGVEPYGQPKYLEIAGKRMAYIDEGKGDAIVFQHGNPTSSYLWRNIMPHLEGLGRLVACDLIGMGASDKLSPSGPDRYSYGEQRDFLFALWDALDLGDHVVLVLHDWGSALGFDWANQHRDRVQGIAFMEAIVTPMTWADWPPAVRGVFQGFRSPQGEPMALEHNIFVERVLPGAILRQLSDEEMNHYRRPFVNGGEDRRPTLSWPRNLPIDGEPAEVVALVNEYRSWLEETDMPKLFINAEPGAIITGRIRDYVRSWPNQTEITVPGVHFVQEDSPEEIGAAIAQFVRRLRSAAG 299
               SCOP domains d2qvbb_ B: automated matches                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2qvbB00 B:3-299  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                     CATH domains
           Pfam domains (1) ------------------------------Abhydrolase_6-2qvbB01 B:33-286                                                                                                                                                                                                                                ------------- Pfam domains (1)
           Pfam domains (2) ------------------------------Abhydrolase_6-2qvbB02 B:33-286                                                                                                                                                                                                                                ------------- Pfam domains (2)
         Sec.struct. author ..........eeeee..eeeeeeee....eeeee.....hhhhhh.hhhhhh...eeeee...................hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhh..hhhhhhhh.hhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qvb B   3 AFGVEPYGQPKYLEIAGKRMAYIDEGKGDAIVFQHGNPTSSYLWRNIMPHLEGLGRLVACDLIGMGASDKLSPSGPDRYSYGEQRDFLFALWDALDLGDHVVLVLHDWGSALGFDWANQHRDRVQGIAFMEAIVTPMTWADWPPAVRGVFQGFRSPQGEPMALEHNIFVERVLPGAILRQLSDEEMNHYRRPFVNGGEDRRPTLSWPRNLPIDGEPAEVVALVNEYRSWLEETDMPKLFINAEPGAIITGRIRDYVRSWPNQTEITVPGVHFVQEDSPEEIGAAIAQFVRRLRSAAG 299
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: AB_hydrolase (347)

(-) Gene Ontology  (6, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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.

Chain A,B   (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.

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  2qvb
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 Related Entries

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

UniProtKB/Swiss-Prot
        DHAA_MYCTO | P9WMR8: 2o2h 2o2i
        DHAA_MYCTU | P9WMR9: 2o2h 2o2i

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2QVB)