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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE COMPLEX OF THE HALOALKANE DEHALOGENASE LINB WITH THE PRODUCT OF DEHALOGENATION REACTION 1,2-DICHLOROPROPANE.
 
Authors :  P. Banas, M. Otyepka, P. Jerabek, J. Vevodova, M. Bohac, J. Damborsky
Date :  09 Dec 04  (Deposition) - 26 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Haloalkane Dehalogenase Linb, 1, 2, 3-Trichloropropane, Hydrolase, Alpha/Beta-Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Minincova, Z. Prokop, J. Vevodova, Y. Nagata, J. Damborsky
Weak Activity Of Haloalkane Dehalogenase Linb With 1, 2, 3-Trichloropropane Revealed By X-Ray Crystallography And Microcalorimetry
Appl. Environ. Microbiol. V. 73 2005 2007
PubMed-ID: 17259360  |  Reference-DOI: 10.1128/AEM.02416-06
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HALOGENALKANE DEHALOGENASE
    Chains: A
    EC Number: 3.8.1.5
    Organism Scientific: SPHINGOMONAS PAUCIMOBILIS
    Organism Taxid: 13689
    Strain: UT26
    Synonym: 1,3,4,6-TETRACHLORO-1,4-CYCLOHEXADIENE HYDROLASE, 1,4-TCDN CHLOROHYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3D2P1Ligand/Ion(2S)-2,3-DICHLOROPROPAN-1-OL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:108 , PRO A:144 , PHE A:151 , ALA A:247 , HIS A:272 , HOH A:2152 , HOH A:2337BINDING SITE FOR RESIDUE D2P A1297
2AC2SOFTWAREASN A:38 , TRP A:109 , PRO A:208 , HOH A:2337BINDING SITE FOR RESIDUE CL A1298
3AC3SOFTWAREHIS A:121 , GLN A:165 , ASP A:166 , HOH A:2157 , HOH A:2207BINDING SITE FOR RESIDUE CA A1299
4AC4SOFTWAREASP A:149 , GLN A:152 , HOH A:2185 , HOH A:2186 , HOH A:2273 , HOH A:2274BINDING SITE FOR RESIDUE CA A1300
5AC5SOFTWAREHOH A:2019 , HOH A:2038 , HOH A:2039 , HOH A:2040BINDING SITE FOR RESIDUE CA A1301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:38 -Pro A:39
2Asp A:73 -Pro A:74
3Thr A:216 -Pro A:217
4Glu A:244 -Pro A:245

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Asymmetric/Biological Unit (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_LINB_SPHPI_001 *A81TLINB_SPHPI  ---  ---AA81T
2UniProtVAR_LINB_SPHPI_002 *A112VLINB_SPHPI  ---  ---AA112V
3UniProtVAR_LINB_SPHPI_003 *I138LLINB_SPHPI  ---  ---AI138L
4UniProtVAR_LINB_SPHPI_004 *A247HLINB_SPHPI  ---  ---AA247H
5UniProtVAR_LINB_SPHPI_005 *M253ILINB_SPHPI  ---  ---AM253I
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2BFN)

(-) 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:294
 aligned with LINB_SPHPI | P51698 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:294
                                    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    
           LINB_SPHPI     3 LGAKPFGEKKFIEIKGRRMAYIDEGTGDPILFQHGNPTSSYLWRNIMPHCAGLGRLIACDLIGMGDSDKLDPSGPERYAYAEHRDYLDALWEALDLGDRVVLVVHDWGSALGFDWARRHRERVQGIAYMEAIAMPIEWADFPEQDRDLFQAFRSQAGEELVLQDNVFVEQVLPGLILRPLSEAEMAAYREPFLAAGEARRPTLSWPRQIPIAGTPADVVAIARDYAGWLSESPIPKLFINAEPGALTTGRMRDFCRTWPNQTEITVAGAHFIQEDSPDEIGAAIAAFVRRLRPA 296
               SCOP domains d2bfna_ A: Haloalkane dehalogenase                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2bfnA00 A:3-296  [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..hhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.....eeeeeeee....hhhhhhhhh....eeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------T------------------------------V-------------------------L------------------------------------------------------------------------------------------------------------H-----I------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2bfn A   3 LGAKPFGEKKFIEIKGRRMAYIDEGTGDPILFQHGNPTSSYLWRNIMPHCAGLGRLIACDLIGMGDSDKLDPSGPERYAYAEHRDYLDALWEALDLGDRVVLVVHDWGSALGFDWARRHRERVQGIAYMEAIAMPIEWADFPEQDRDLFQAFRSQAGEELVLQDNVFVEQVLPGLILRPLSEAEMAAYREPFLAAGEARRPTLSWPRQIPIAGTPADVVAIARDYAGWLSESPIPKLFINAEPGALTTGRMRDFCRTWPNQTEITVAGAHFIQEDSPDEIGAAIAAFVRRLRPA 296
                                    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, 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  (0, 0)

(no "Pfam Domain" information available for 2BFN)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LINB_SPHPI | P51698)
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:0009636    response to toxic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        LINB_SPHPI | P51698: 1cv2 1d07 1g42 1g4h 1g5f 1iz7 1iz8 1k5p 1k63 1k6e 1mj5 4wdq

(-) Related Entries Specified in the PDB File

1cv2 HYDROLYTIC HALOALKANE DEHALOGENASE LINB FROM SPHINGOMONAS PAUCIMOBILIS UT26 AT 1.6 A RESOLUTION
1d07 HYDROLYTIC HALOALKANE DEHALOGENASE LINB FROM SPHINGOMONAS PAUCIMOBILIS UT26 WITH 1,3- PROPANEDIOL, A PRODUCT OF DEBROMIDATION OF DIBROMPROPANE, AT 2.0A RESOLUTION
1g42 STRUCTURE OF 1,3,4,6-TETRACHLORO-1,4- CYCLOHEXADIENEHYDROLASE (LINB) FROM SPHINGOMONAS PAUCIMOBILIS COMPLEXEDWITH 1,2-DICHLOROPROPANE
1g4h LINB COMPLEXED WITH BUTAN-1-OL
1g5f STRUCTURE OF LINB COMPLEXED WITH 1,2- DICHLOROETHANE
1iz7 RE-REFINEMENT OF THE STRUCTURE OF HYDROLYTIC HALOALKANEDEHALOGENASE LINB FROM SPHINGOMONAS PAUCIMOBILIS UT26 AT1.6 A RESOLUTION
1iz8 RE-REFINEMENT OF THE STRUCTURE OF HYDROLYTIC HALOALKANEDEHALOGENASE LINB FROM SPHINGOMONAS PAUCIMOBILIS UT26 WITH1,3-PROPANEDIOL, A PRODUCT OF DEBROMIDATION OFDIBROMPROPANE, AT 2 .0A RESOLUTION
1k5p HYDROLYTIC HALOALKANE DEHALOGENASE LINB FROM SPHINGOMONASPAUCIMOBILIS UT26 AT 1.8A RESOLUTION
1k63 COMPLEX OF HYDROLYTIC HALOALKANE DEHALOGENASE LINB FROMSPHINGOMONAS PAUCIMOBILIS WITH UT26 2 -BROMO-2-PROPENE-1-OLAT 1.8A RESOLUTION
1k6e COMPLEX OF HYDROLYTIC HALOALKANE DEHALOGENASE LINB FROMSPHINGOMONAS PAUCIMOBILIS UT26 WITH 1 ,2-PROPANEDIOL(PRODUCT OF DEHALOGENATION OF 1,2-DIBROMOPROPANE) AT 1.85A
1mj5 LINB (HALOALKANE DEHALOGENASE) FROM SPHINGOMONASPAUCIMOBILIS UT26 AT ATOMIC RESOLUTION