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(-)Asym./Biol. Unit
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(-) Description

Title :  NATIVE L-HALOACID DEHALOGENASE FROM A RHODOBACTERACEAE FAMILY BACTERIUM
 
Authors :  H. R. Novak, C. Sayer, M. N. Isupov, K. Paszkiewicz, D. Gotz, A. M. Spragg J. A. Littlechild
Date :  09 Oct 12  (Deposition) - 01 May 13  (Release) - 01 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. R. Novak, C. Sayer, M. N. Isupov, K. Paszkiewicz, D. Gotz, A. Mearns Spragg, J. A. Littlechild
Marine Rhodobacteraceae L-Haloacid Dehalogenase Contains A Novel His/Glu Dyad That Could Activate The Catalytic Water.
Febs J. V. 280 1664 2013
PubMed-ID: 23384397  |  Reference-DOI: 10.1111/FEBS.12177

(-) Compounds

Molecule 1 - L-HALOACID DEHALOGENASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: RIPL
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Organism Scientific: RHODOBACTERACEAE
    Organism Taxid: 31989

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2YML)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:131 -Pro A:132
2Lys A:157 -Pro A:158
3Ala B:131 -Pro B:132
4Lys B:157 -Pro B:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YML)

(-) 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:228
 aligned with R4GRT2_9RHOB | R4GRT2 from UniProtKB/TrEMBL  Length:236

    Alignment length:228
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228        
         R4GRT2_9RHOB     9 PSRSGILVFDVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACHIWDTIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASLTA 236
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhhh..eeeeee........hhhhhh.hhhhh.eeee.hhhh....hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhh...eeeee.................eee.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yml A   9 PSRSGILVFDVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACHIWDTIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASLTA 236
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228        


Chain B from PDB  Type:PROTEIN  Length:224
 aligned with R4GRT2_9RHOB | R4GRT2 from UniProtKB/TrEMBL  Length:236

    Alignment length:224
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    
         R4GRT2_9RHOB    11 RSGILVFDVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACHIWDTIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASL 234
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhhh..eeeeee........hhhhhh.hhhhh.eeee.hhhh....hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhh...eeeee.................eee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yml B  11 RSGILVFDVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACHIWDTIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASL 234
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
   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  (0, 0)

(no "SCOP Domain" information available for 2YML)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YML)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (R4GRT2_9RHOB | R4GRT2)
molecular function
    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.
    GO:0019120    hydrolase activity, acting on acid halide bonds, in C-halide compounds    Catalysis of the hydrolysis of any acid halide bond in substances containing halogen atoms in organic linkage.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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  Sites
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  Cis Peptide Bonds
    Ala A:131 - Pro A:132   [ RasMol ]  
    Ala B:131 - Pro B:132   [ RasMol ]  
    Lys A:157 - Pro A:158   [ RasMol ]  
    Lys B:157 - Pro B:158   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        R4GRT2_9RHOB | R4GRT2: 2ymm 2ymp 2ymq 2yn4 4ce6 4cf3 4cf4 4cf5 4cnq

(-) Related Entries Specified in the PDB File

2ymm SULFATE BOUND L-HALOACID DEHALOGENASE FROM A RHODOBACTERACEAE FAMILY BACTERIUM
2ymp CHLOROACETIC ACID COMPLEX BOUND L-HALOACID DEHALOGENASE FROM A RHODOBACTERACEAE FAMILY BACTERIUM
2ymq CHLOROPROPIONIC ACID COMPLEX BOUND L-HALOACID DEHALOGENASE FROM A RHODOBACTERACEAE FAMILY BACTERIUM
2yn4 L-2-CHLOROBUTRYIC ACID BOUND COMPLEX L-HALOACID DEHALOGENASE FROM A RHODOBACTERACEAE FAMILY BACTERIUM