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(-) Description

Title :  CRYSTAL STRUCTURE OF DBJA (WILD TYPE TYPE I)
 
Authors :  Y. Sato, T. Senda
Date :  23 May 09  (Deposition) - 26 May 10  (Release) - 27 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym./Biol. Unit :  A,B
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
    Chains: A, B
    EC Number: 3.8.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PYBJA3
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DBJA
    Organism Scientific: BRADYRHIZOBIUM JAPONICUM
    Organism Taxid: 375
    Strain: USDA110

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2SUC3Ligand/IonSUCROSE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:38 , TRP A:104 , PHE A:213 , PRO A:214BINDING SITE FOR RESIDUE CL A 401
2AC2SOFTWAREPRO A:30 , VAL A:55 , ALA A:299 , GLU A:302 , HOH A:600 , HOH A:605 , HOH A:775 , HOH A:824 , ARG B:269 , CYS B:270 , ALA B:271BINDING SITE FOR RESIDUE SUC A 2381
3AC3SOFTWAREGLU A:261 , ALA A:264 , ALA A:265 , CYS A:270 , ALA A:271 , LEU A:272 , HOH A:570 , HOH A:702 , HOH A:924 , ALA B:26 , ASP B:28 , ALA B:29 , PRO B:54 , SUC B:2380BINDING SITE FOR RESIDUE SUC A 2382
4AC4SOFTWAREASN B:38 , TRP B:104 , PHE B:213 , PRO B:214 , HOH B:773BINDING SITE FOR RESIDUE CL B 402
5AC5SOFTWAREARG A:269 , CYS A:270 , ALA A:271 , HOH A:536 , HOH A:555 , HOH A:924 , SUC A:2382 , PRO B:30 , VAL B:55 , ALA B:299 , GLU B:302 , ALA B:303 , HOH B:563BINDING SITE FOR RESIDUE SUC B 2380

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3A2M)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological 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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3A2M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3A2M)

(-) Exons   (0, 0)

(no "Exon" information available for 3A2M)

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

    Alignment length:298
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297        
           DHAA_BRADU     8 EIRRAPVLGSSMAYRETGAQDAPVVLFLHGNPTSSHIWRNILPLVSPVAHCIAPDLIGFGQSGKPDIAYRFFDHVRYLDAFIEQRGVTSAYLVAQDWGTALAFHLAARRPDFVRGLAFMEFIRPMPTWQDFHHTEVAEEQDHAEAARAVFRKFRTPGEGEAMILEANAFVERVLPGGIVRKLGDEEMAPYRTPFPTPESRRPVLAFPRELPIAGEPADVYEALQSAHAALAASSYPKLLFTGEPGALVSPEFAERFAASLTRCALIRLGAGLHYLQEDHADAIGRSVAGWIAGIEAVR 305
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3a2mA00 A:8-305  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..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
                 3a2m A   8 EIRRAPVLGSSMAYRETGAQDAPVVLFLHGNPTSSHIWRNILPLVSPVAHCIAPDLIGFGQSGKPDIAYRFFDHVRYLDAFIEQRGVTSAYLVAQDWGTALAFHLAARRPDFVRGLAFMEFIRPMPTWQDFHHTEVAEEQDHAEAARAVFRKFRTPGEGEAMILEANAFVERVLPGGIVRKLGDEEMAPYRTPFPTPESRRPVLAFPRELPIAGEPADVYEALQSAHAALAASSYPKLLFTGEPGALVSPEFAERFAASLTRCALIRLGAGLHYLQEDHADAIGRSVAGWIAGIEAVR 305
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297        


Chain B from PDB  Type:PROTEIN  Length:300
 aligned with DHAA_BRADU | P59337 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:300
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305
           DHAA_BRADU     6 EIEIRRAPVLGSSMAYRETGAQDAPVVLFLHGNPTSSHIWRNILPLVSPVAHCIAPDLIGFGQSGKPDIAYRFFDHVRYLDAFIEQRGVTSAYLVAQDWGTALAFHLAARRPDFVRGLAFMEFIRPMPTWQDFHHTEVAEEQDHAEAARAVFRKFRTPGEGEAMILEANAFVERVLPGGIVRKLGDEEMAPYRTPFPTPESRRPVLAFPRELPIAGEPADVYEALQSAHAALAASSYPKLLFTGEPGALVSPEFAERFAASLTRCALIRLGAGLHYLQEDHADAIGRSVAGWIAGIEAVR 305
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3a2mB00 B:6-305  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee..eeeeeeee......eeeee.....hhhhhh.hhhhhh...eeeee...............hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhh.....hhhhhhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhh..eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3a2m B   6 EIEIRRAPVLGSSMAYRETGAQDAPVVLFLHGNPTSSHIWRNILPLVSPVAHCIAPDLIGFGQSGKPDIAYRFFDHVRYLDAFIEQRGVTSAYLVAQDWGTALAFHLAARRPDFVRGLAFMEFIRPMPTWQDFHHTEVAEEQDHAEAARAVFRKFRTPGEGEAMILEANAFVERVLPGGIVRKLGDEEMAPYRTPFPTPESRRPVLAFPRELPIAGEPADVYEALQSAHAALAASSYPKLLFTGEPGALVSPEFAERFAASLTRCALIRLGAGLHYLQEDHADAIGRSVAGWIAGIEAVR 305
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305
   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 3A2M)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3A2M)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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 | P59337: 3a2l 3a2n 3afi

(-) Related Entries Specified in the PDB File

3a1o HIS-DBJA
3a2l MUTANT DBJA DELTA
3a2n DBJA (WILD TYPE, TYPE II)