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(-) Description

Title :  CRYSTAL STRUCTURE OF DBJA (WILD TYPE TYPE II P21)
 
Authors :  Y. Sato, T. Senda
Date :  23 May 09  (Deposition) - 26 May 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym. Unit :  A,B,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  E,F  (1x)
Keywords :  A/B-Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. Prokop, Y. Sato, J. Brezovsky, T. Mozga, R. Chaloupkova, T. Koudelakova, P. Jerabek, V. Stepankova, R. Natsume, J. G. Van Leeuwen, D. B. Janssen, J. Florian, Y. Nagata, T. Senda, J. Damborsky
Enantioselectivity Of Haloalkane Dehalogenases And Its Modulation By Surface Loop Engineering
Angew. Chem. Int. Ed. Engl. V. 49 6111 2010
PubMed-ID: 20645368  |  Reference-DOI: 10.1002/ANIE.201001753

(-) Compounds

Molecule 1 - HALOALKANE DEHALOGENASE
    ChainsA, B, E, F
    EC Number3.8.1.5
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPYBJA3
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneDBJA
    Organism ScientificBRADYRHIZOBIUM JAPONICUM
    Organism Taxid375
    StrainUSDA110

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABEF
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:38 , TRP A:104 , PRO A:214 , HOH A:409BINDING SITE FOR RESIDUE CL A 313
2AC2SOFTWAREASN B:38 , TRP B:104 , PRO B:214BINDING SITE FOR RESIDUE CL B 313
3AC3SOFTWAREASN F:38 , TRP F:104 , PHE F:213 , PRO F:214BINDING SITE FOR RESIDUE CL F 313

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3A2N)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Asn A:38 -Pro A:39
2Glu A:222 -Pro A:223
3Glu A:250 -Pro A:251
4Asn B:38 -Pro B:39
5Glu B:222 -Pro B:223
6Glu B:250 -Pro B:251
7Asn E:38 -Pro E:39
8Glu E:222 -Pro E:223
9Glu E:250 -Pro E:251
10Asn F:38 -Pro F:39
11Glu F:222 -Pro F:223
12Glu F:250 -Pro F:251

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3A2N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3A2N)

(-) Exons   (0, 0)

(no "Exon" information available for 3A2N)

(-) Sequences/Alignments

Asymmetric 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:298
 aligned with DHAA_BRADU | P59337 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:298
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299        
           DHAA_BRADU    10 RRAPVLGSSMAYRETGAQDAPVVLFLHGNPTSSHIWRNILPLVSPVAHCIAPDLIGFGQSGKPDIAYRFFDHVRYLDAFIEQRGVTSAYLVAQDWGTALAFHLAARRPDFVRGLAFMEFIRPMPTWQDFHHTEVAEEQDHAEAARAVFRKFRTPGEGEAMILEANAFVERVLPGGIVRKLGDEEMAPYRTPFPTPESRRPVLAFPRELPIAGEPADVYEALQSAHAALAASSYPKLLFTGEPGALVSPEFAERFAASLTRCALIRLGAGLHYLQEDHADAIGRSVAGWIAGIEAVRPQ 307
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3a2nA00 A:10-307  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeeeeee......eeeee.....hhhhhh.hhhhhh...eeeee...............hhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhh......hhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhh.....hhhhhhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhh..eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a2n A  10 RRAPVLGSSMAYRETGAQDAPVVLFLHGNPTSSHIWRNILPLVSPVAHCIAPDLIGFGQSGKPDIAYRFFDHVRYLDAFIEQRGVTSAYLVAQDWGTALAFHLAARRPDFVRGLAFMEFIRPMPTWQDFHHTEVAEEQDHAEAARAVFRKFRTPGEGEAMILEANAFVERVLPGGIVRKLGDEEMAPYRTPFPTPESRRPVLAFPRELPIAGEPADVYEALQSAHAALAASSYPKLLFTGEPGALVSPEFAERFAASLTRCALIRLGAGLHYLQEDHADAIGRSVAGWIAGIEAVRPQ 307
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299        

Chain B from PDB  Type:PROTEIN  Length:298
 aligned with DHAA_BRADU | P59337 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:298
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299        
           DHAA_BRADU    10 RRAPVLGSSMAYRETGAQDAPVVLFLHGNPTSSHIWRNILPLVSPVAHCIAPDLIGFGQSGKPDIAYRFFDHVRYLDAFIEQRGVTSAYLVAQDWGTALAFHLAARRPDFVRGLAFMEFIRPMPTWQDFHHTEVAEEQDHAEAARAVFRKFRTPGEGEAMILEANAFVERVLPGGIVRKLGDEEMAPYRTPFPTPESRRPVLAFPRELPIAGEPADVYEALQSAHAALAASSYPKLLFTGEPGALVSPEFAERFAASLTRCALIRLGAGLHYLQEDHADAIGRSVAGWIAGIEAVRPQ 307
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3a2nB00 B:10-307  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeeeeee......eeeee.....hhhhhh.hhhhhh...eeeee...............hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhhh.....hhhhhhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhh..eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a2n B  10 RRAPVLGSSMAYRETGAQDAPVVLFLHGNPTSSHIWRNILPLVSPVAHCIAPDLIGFGQSGKPDIAYRFFDHVRYLDAFIEQRGVTSAYLVAQDWGTALAFHLAARRPDFVRGLAFMEFIRPMPTWQDFHHTEVAEEQDHAEAARAVFRKFRTPGEGEAMILEANAFVERVLPGGIVRKLGDEEMAPYRTPFPTPESRRPVLAFPRELPIAGEPADVYEALQSAHAALAASSYPKLLFTGEPGALVSPEFAERFAASLTRCALIRLGAGLHYLQEDHADAIGRSVAGWIAGIEAVRPQ 307
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299        

Chain E from PDB  Type:PROTEIN  Length:298
 aligned with DHAA_BRADU | P59337 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:298
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299        
           DHAA_BRADU    10 RRAPVLGSSMAYRETGAQDAPVVLFLHGNPTSSHIWRNILPLVSPVAHCIAPDLIGFGQSGKPDIAYRFFDHVRYLDAFIEQRGVTSAYLVAQDWGTALAFHLAARRPDFVRGLAFMEFIRPMPTWQDFHHTEVAEEQDHAEAARAVFRKFRTPGEGEAMILEANAFVERVLPGGIVRKLGDEEMAPYRTPFPTPESRRPVLAFPRELPIAGEPADVYEALQSAHAALAASSYPKLLFTGEPGALVSPEFAERFAASLTRCALIRLGAGLHYLQEDHADAIGRSVAGWIAGIEAVRPQ 307
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3a2nE00 E:10-307  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeeeeee......eeeee.....hhhhhh.hhhhhh...eeeee...............hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee...................hhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhh.....hhhhhhhhhh...hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhh..eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a2n E  10 RRAPVLGSSMAYRETGAQDAPVVLFLHGNPTSSHIWRNILPLVSPVAHCIAPDLIGFGQSGKPDIAYRFFDHVRYLDAFIEQRGVTSAYLVAQDWGTALAFHLAARRPDFVRGLAFMEFIRPMPTWQDFHHTEVAEEQDHAEAARAVFRKFRTPGEGEAMILEANAFVERVLPGGIVRKLGDEEMAPYRTPFPTPESRRPVLAFPRELPIAGEPADVYEALQSAHAALAASSYPKLLFTGEPGALVSPEFAERFAASLTRCALIRLGAGLHYLQEDHADAIGRSVAGWIAGIEAVRPQ 307
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299        

Chain F from PDB  Type:PROTEIN  Length:299
 aligned with DHAA_BRADU | P59337 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:299
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298         
           DHAA_BRADU     9 IRRAPVLGSSMAYRETGAQDAPVVLFLHGNPTSSHIWRNILPLVSPVAHCIAPDLIGFGQSGKPDIAYRFFDHVRYLDAFIEQRGVTSAYLVAQDWGTALAFHLAARRPDFVRGLAFMEFIRPMPTWQDFHHTEVAEEQDHAEAARAVFRKFRTPGEGEAMILEANAFVERVLPGGIVRKLGDEEMAPYRTPFPTPESRRPVLAFPRELPIAGEPADVYEALQSAHAALAASSYPKLLFTGEPGALVSPEFAERFAASLTRCALIRLGAGLHYLQEDHADAIGRSVAGWIAGIEAVRPQ 307
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3a2nF00 F:9-307  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeeeeee......eeeee.....hhhhhh.hhhhhh...eeeee...............hhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhh.....hhhhhhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhh...eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a2n F   9 IRRAPVLGSSMAYRETGAQDAPVVLFLHGNPTSSHIWRNILPLVSPVAHCIAPDLIGFGQSGKPDIAYRFFDHVRYLDAFIEQRGVTSAYLVAQDWGTALAFHLAARRPDFVRGLAFMEFIRPMPTWQDFHHTEVAEEQDHAEAARAVFRKFRTPGEGEAMILEANAFVERVLPGGIVRKLGDEEMAPYRTPFPTPESRRPVLAFPRELPIAGEPADVYEALQSAHAALAASSYPKLLFTGEPGALVSPEFAERFAASLTRCALIRLGAGLHYLQEDHADAIGRSVAGWIAGIEAVRPQ 307
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298         

   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 3A2N)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3A2N)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,E,F   (DHAA_BRADU | P59337)
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.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
biological process
    GO:0042206    halogenated hydrocarbon catabolic process    The chemical reactions and pathways resulting in the breakdown of halogenated hydrocarbons, any hydrocarbon with one or more halogen atoms attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DHAA_BRADU | P593373a2l 3a2m 3afi

(-) Related Entries Specified in the PDB File

3a1o HIS-DBJA
3a2l MUTANT DBJA
3a2m DBJA (WILD TYPE, TYPE I)