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(-) Description

Title :  THE EFFECT OF DEUTERATION ON PROTEIN STRUCTURE A HIGH RESOLUTION COMPARISON OF HYDROGENOUS AND PERDEUTERATED HALOALKANE DEHALOGENASE
 
Authors :  X. Liu, L. Hanson, P. Langan, R. E. Viola
Date :  18 Apr 07  (Deposition) - 04 Sep 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  X
Keywords :  Protein Deuteration, Haloalkane Dehalogenase, High Resolution Structure, Catalytic Mechanism, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Liu, B. L. Hanson, P. Langan, R. E. Viola
The Effect Of Deuteration On Protein Structure: A High-Resolution Comparison Of Hydrogenous And Perdeuterated Haloalkane Dehalogenase.
Acta Crystallogr. , Sect. D V. 63 1000 2007
PubMed-ID: 17704569  |  Reference-DOI: 10.1107/S0907444907037705
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HALOALKANE DEHALOGENASE
    Chains: X
    EC Number: 3.8.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PCHC109
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DHLA
    Organism Scientific: XANTHOBACTER AUTOTROPHICUS
    Organism Taxid: 280
    Strain: GJ10

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2PKY)

(-) Sites  (0, 0)

(no "Site" information available for 2PKY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu X:56 -Pro X:57
2Gln X:167 -Pro X:168

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PKY)

(-) 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 X from PDB  Type:PROTEIN  Length:308
 aligned with DHLA_XANAU | P22643 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:308
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301        
           DHLA_XANAU     2 INAIRTPDQRFSNLDQYPFSPNYLDDLPGYPGLRAHYLDEGNSDAEDVFLCLHGEPTWSYLYRKMIPVFAESGARVIAPDFFGFGKSDKPVDEEDYTFEFHRNFLLALIERLDLRNITLVVQDWGGFLGLTLPMADPSRFKRLIIMNACLMTDPVTQPAFSAFVTQPADGFTAWKYDLVTPSDLRLDQFMKRWAPTLTEAEASAYAAPFPDTSYQAGVRKFPKMVAQRDQACIDISTEAISFWQNDWNGQTFMAIGMKDKLLGPDVMYPMKALINGCPEPLEIADAGHFVQEFGEQVAREALKHFAET 309
               SCOP domains d2pkyx_ X: Haloalkane dehalogenase                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2pkyX00 X:2-309  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..hhhhhh.........eee..........eeeeee.......eeeee.....hhhhhh.hhhhhhhh..eeeee.........ee.hhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhh.eeeeeee...........hhhhhh......hhhhhhhhhhh....hhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhh......eee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pky X   2 INAIRTPDQRFSNLDQYPFSPNYLDDLPGYPGLRAHYLDEGNSDAEDVFLCLHGEPTWSYLYRKMIPVFAESGARVIAPDFFGFGKSDKPVDEEDYTFEFHRNFLLALIERLDLRNITLVVQDWGGFLGLTLPMADPSRFKRLIIMNACLMTDPVTQPAFSAFVTQPADGFTAWKYDLVTPSDLRLDQFMKRWAPTLTEAEASAYAAPFPDTSYQAGVRKFPKMVAQRDQACIDISTEAISFWQNDWNGQTFMAIGMKDKLLGPDVMYPMKALINGCPEPLEIADAGHFVQEFGEQVAREALKHFAET 309
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301
   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 2PKY)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (DHLA_XANAU | P22643)
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:0019260    1,2-dichloroethane catabolic process    The chemical reactions and pathways resulting in the breakdown of 1,2-dichloroethane, a major commodity chemical used, for example, in the manufacture of vinyl chloride.
    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.

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  Cis Peptide Bonds
    Gln X:167 - Pro X:168   [ RasMol ]  
    Glu X:56 - Pro X:57   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        DHLA_XANAU | P22643: 1b6g 1be0 1bee 1bez 1cij 1edb 1edd 1ede 1hde 2dhc 2dhd 2dhe 2eda 2edc 2had 2yxp

(-) Related Entries Specified in the PDB File

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