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(-) Description

Title :  HYDROLYTIC HALOALKANE DEHALOGENASE LINB FROM SPHINGOMONAS PAUCIMOBILIS UT26 WITH 1,3-PROPANEDIOL, A PRODUCT OF DEBROMIDATION OF DIBROMPROPANE, AT 2.0A RESOLUTION
 
Authors :  J. Marek, J. Vevodova, J. Damborsky, I. Smatanova, L. A. Svensson, J. Newman, Y. Nagata, M. Takagi
Date :  09 Sep 99  (Deposition) - 11 Sep 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Dehalogenase, Lindane, Biodegradation, Alpha/Beta-Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Marek, J. Vevodova, I. K. Smatanova, Y. Nagata, L. A. Svensson, J. Newman, M. Takagi, J. Damborsky
Crystal Structure Of The Haloalkane Dehalogenase From Sphingomonas Paucimobilis Ut26.
Biochemistry V. 39 14082 2000
PubMed-ID: 11087355  |  Reference-DOI: 10.1021/BI001539C
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HALOALKANE DEHALOGENASE
    Chains: A
    EC Number: 3.8.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMYLB1
    Expression System Strain: HB101
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: SPHINGOMONAS PAUCIMOBILIS
    Organism Taxid: 13689
    Strain: UT26
    Synonym: LINB, 1,3,4,6-TETRACHLORO-1,4-CYCLOHEXADIENE HYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1BR2Ligand/IonBROMIDE ION
2PDO1Ligand/Ion1,3-PROPANDIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:38 , TRP A:109 , PHE A:169 , PRO A:208 , PDO A:903BINDING SITE FOR RESIDUE BR A 901
2AC2SOFTWAREGLN A:165 , ASP A:166 , PRO A:175 , ILE A:178 , HOH A:1007 , HOH A:1028BINDING SITE FOR RESIDUE BR A 902
3AC3SOFTWAREASN A:38 , ASP A:108 , PHE A:151 , PHE A:169 , VAL A:173 , HIS A:272 , PHE A:273 , BR A:901BINDING SITE FOR RESIDUE PDO A 903

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1D07)

(-) Cis Peptide Bonds  (5, 5)

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
5Pro A:295 -Ala A:296

 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 1D07)

(-) Exons   (0, 0)

(no "Exon" information available for 1D07)

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

    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   
           LINB_SPHPI     4 GAKPFGEKKFIEIKGRRMAYIDEGTGDPILFQHGNPTSSYLWRNIMPHCAGLGRLIACDLIGMGDSDKLDPSGPERYAYAEHRDYLDALWEALDLGDRVVLVVHDWGSALGFDWARRHRERVQGIAYMEAIAMPIEWADFPEQDRDLFQAFRSQAGEELVLQDNVFVEQVLPGLILRPLSEAEMAAYREPFLAAGEARRPTLSWPRQIPIAGTPADVVAIARDYAGWLSESPIPKLFINAEPGALTTGRMRDFCRTWPNQTEITVAGAHFIQEDSPDEIGAAIAAFVRRLRPA 296
               SCOP domains d1d07a_ A: Haloalkane dehalogenase                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1d07A00 A:4-296  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee......eeeeee...eeeeeee.....hhhhhhhhhhhh...eeeeee...................hhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhh....eeeeeee.............hhhhhhhhhhh...hhhhhh...hhhhhhhhhh......hhhhhhhhh.........hhhhhhhhhh......hhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhh....eeeeeeee...hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------T------------------------------V-------------------------L------------------------------------------------------------------------------------------------------------H-----I------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d07 A   4 GAKPFGEKKFIEIKGRRMAYIDEGTGDPILFQHGNPTSSYLWRNIMPHCAGLGRLIACDLIGMGDSDKLDPSGPERYAYAEHRDYLDALWEALDLGDRVVLVVHDWGSALGFDWARRHRERVQGIAYMEAIAMPIEWADFPEQDRDLFQAFRSQAGEELVLQDNVFVEQVLPGLILRPLSEAEMAAYREPFLAAGEARRPTLSWPRQIPIAGTPADVVAIARDYAGWLSESPIPKLFINAEPGALTTGRMRDFCRTWPNQTEITVAGAHFIQEDSPDEIGAAIAAFVRRLRPA 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  (0, 0)

(no "Pfam Domain" information available for 1D07)

(-) 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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  1d07
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 Related Entries

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

UniProtKB/Swiss-Prot
        LINB_SPHPI | P51698: 1cv2 1g42 1g4h 1g5f 1iz7 1iz8 1k5p 1k63 1k6e 1mj5 2bfn 4wdq

(-) Related Entries Specified in the PDB File

1cv2