Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  MUTAGENESIS OF A RHODOBACTERACEAE L-HALOACID DEHALOGENASE
 
Authors :  H. R. Novak, C. Sayer, M. N. Isupov, J. A. Littlechild
Date :  08 Nov 13  (Deposition) - 19 Nov 14  (Release) - 19 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
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 (DE3)-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 4CE6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CE6)

(-) 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 4CE6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CE6)

(-) Exons   (0, 0)

(no "Exon" information available for 4CE6)

(-) 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:226
 aligned with M9P6K0_9RHOB | M9P6K0 from UniProtKB/TrEMBL  Length:236

    Alignment length:226
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      
         M9P6K0_9RHOB    11 RSGILVFDVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACHIWDTIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASLTA 236
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhh..eeeeee........hhhhhh.hhhhh.eeee.........hhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhh...eeeee.................eee.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ce6 A  11 RSGILVFdVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACNIWDTIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASLTA 236
                                   |20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      
                                  18-ASB                                                                                                                                                                                                                      


Chain A from PDB  Type:PROTEIN  Length:226
 aligned with R4GRT2_9RHOB | R4GRT2 from UniProtKB/TrEMBL  Length:236

    Alignment length:226
                                    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 RSGILVFDVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACHIWDTIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASLTA 236
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhh..eeeeee........hhhhhh.hhhhh.eeee.........hhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhh...eeeee.................eee.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ce6 A  11 RSGILVFdVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACNIWDTIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASLTA 236
                                   |20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      
                                  18-ASB                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:224
 aligned with M9P6K0_9RHOB | M9P6K0 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    
         M9P6K0_9RHOB    11 RSGILVFDVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACHIWDTIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASL 234
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.......hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...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
                 4ce6 B  11 RSGILVFdVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACNIWDTIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASL 234
                                   |20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    
                                  18-ASB                                                                                                                                                                                                                    


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.......hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...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
                 4ce6 B  11 RSGILVFdVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACNIWDTIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASL 234
                                   |20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    
                                  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 4CE6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CE6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CE6)

(-) Gene Ontology  (4, 7)

Asymmetric/Biological Unit(hide GO term definitions)
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.

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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ASB  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 4ce6)
 
  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 ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4ce6
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  M9P6K0_9RHOB | M9P6K0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  R4GRT2_9RHOB | R4GRT2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.8.1.2
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  M9P6K0_9RHOB | M9P6K0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  R4GRT2_9RHOB | R4GRT2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        M9P6K0_9RHOB | M9P6K0: 4cf3 4cf4 4cf5
UniProtKB/TrEMBL
        R4GRT2_9RHOB | R4GRT2: 2yml 2ymm 2ymp 2ymq 2yn4 4cf3 4cf4 4cf5 4cnq

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4CE6)