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(-) Description

Title :  MUTAGENESIS OF A RHODOBACTERACEAE L-HALOACID DEHALOGENASE
 
Authors :  H. R. Novak, C. Sayer, M. N. Isupov, J. A. Littlechild
Date :  13 Nov 13  (Deposition) - 26 Nov 14  (Release) - 26 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.14
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. R. Novak, C. Sayer, M. N. Isupov, J. A. Littlechild
Mutagenesis Of A Rhodobacteraceae L-Haloacid Dehalogenase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - L-HALOACID DEHALOGENASE
    Chains: A, B
    EC Number: 3.8.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: CODONPLUS-RIPL
    Expression System Vector: PET-28A
    Expression System Vector Type: PLASMID
    Mutation: YES
    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  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ASB2Mod. Amino AcidASPARTIC ACID-4-CARBOXYMETHYL ESTER

(-) Sites  (0, 0)

(no "Site" information available for 4CF4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CF4)

(-) 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 4CF4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CF4)

(-) Exons   (0, 0)

(no "Exon" information available for 4CF4)

(-) 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:223
 aligned with M9P6K0_9RHOB | M9P6K0 from UniProtKB/TrEMBL  Length:236

    Alignment length:223
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232   
         M9P6K0_9RHOB    13 GILVFDVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACHIWDTIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASLT 235
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhhh..eeeeee........hhhhhh.hhhhh.eeee.........hhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhh...eeeee.................eee.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cf4 A  13 GILVFdVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACHIWATIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASLT 235
                                 |  22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232   
                                 |                                                                                                                                                                                                                         
                                18-ASB                                                                                                                                                                                                                     


Chain A from PDB  Type:PROTEIN  Length:223
 aligned with R4GRT2_9RHOB | R4GRT2 from UniProtKB/TrEMBL  Length:236

    Alignment length:223
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232   
         R4GRT2_9RHOB    13 GILVFDVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACHIWDTIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASLT 235
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhhh..eeeeee........hhhhhh.hhhhh.eeee.........hhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhh...eeeee.................eee.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cf4 A  13 GILVFdVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACHIWATIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASLT 235
                                 |  22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232   
                                18-ASB                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:223
 aligned with M9P6K0_9RHOB | M9P6K0 from UniProtKB/TrEMBL  Length:236

    Alignment length:223
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232   
         M9P6K0_9RHOB    13 GILVFDVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACHIWDTIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASLT 235
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhhh..eeeeee........hhhhhh.hhhhh.eeee.........hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhh...eeeee.................eee.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cf4 B  13 GILVFdVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACHIWATIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASLT 235
                                 |  22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232   
                                18-ASB                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:223
 aligned with R4GRT2_9RHOB | R4GRT2 from UniProtKB/TrEMBL  Length:236

    Alignment length:223
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232   
         R4GRT2_9RHOB    13 GILVFDVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACHIWDTIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASLT 235
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhhh..eeeeee........hhhhhh.hhhhh.eeee.........hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhh...eeeee.................eee.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cf4 B  13 GILVFdVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACHIWATIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASLT 235
                                 |  22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232   
                                18-ASB
   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 4CF4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CF4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CF4)

(-) Gene Ontology  (4, 7)

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.

Chain A,B   (M9P6K0_9RHOB | M9P6K0)
molecular function
    GO:0018784    (S)-2-haloacid dehalogenase activity    Catalysis of the reaction: (S)-2-haloacid + H2O = (R)-2-hydroxyacid + 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.
    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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  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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  R4GRT2_9RHOB | R4GRT2
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 Related Entries

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

UniProtKB/Swiss-Prot
        M9P6K0_9RHOB | M9P6K0: 4ce6 4cf3 4cf5
UniProtKB/TrEMBL
        R4GRT2_9RHOB | R4GRT2: 2yml 2ymm 2ymp 2ymq 2yn4 4ce6 4cf3 4cf5 4cnq

(-) Related Entries Specified in the PDB File

4ce6 MUTAGENESIS OF A RHODOBACTERACEAE L-HALOACID DEHALOGENASE
4cf3 MUTAGENESIS OF A RHODOBACTERACEAE L-HALOACID DEHALOGENASE
4cf5 MUTAGENESIS OF A RHODOBACTERACEAE L-HALOACID DEHALOGENASE