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(-) Description

Title :  CRYSTAL STRUCTURE OF HALOALKANE DEHALOGENASE DBEA FROM BRADYRHIZOBIUM ELKANI USDA94
 
Authors :  T. Prudnikova, R. Chaloupkova, P. Rezacova, T. Mozga, T. Koudelakova, M. Kuty, Y. Nagata, J. Damborsky, I. Kuta Smatanova, Structure 2 Fu Project (S2F)
Date :  08 Apr 13  (Deposition) - 25 Jun 14  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Structural Genomics, Enzyme Function Initiative, Structure 2 Function Project, S2F, Two Domain Organization, Dimer Catalytic Pentad, Hydrolase, Halogen Binding, (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Chaloupkova, T. Prudnikova, P. Rezacova, Z. Prokop, T. Koudelakova, L. Daniel, J. Brezovsky, W. Ikeda-Ohtsubo, Y. Sato, M. Kuty, Y. Nagata, I. Kuta Smatanova, J. Damborsky
Structural And Functional Analysis Of A Novel Haloalkane Dehalogenase With Two Halide-Binding Sites.
Acta Crystallogr. , Sect. D V. 70 1884 2014
PubMed-ID: 25004965  |  Reference-DOI: 10.1107/S1399004714009018

(-) Compounds

Molecule 1 - HALOALKANE DEHALOGENASE
    Chains: A, B, C, D
    EC Number: 3.8.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DBEA, DHAA
    Organism Scientific: BRADYRHIZOBIUM ELKANII
    Organism Taxid: 29448
    Strain: USDA94

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2CL8Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:38 , TRP A:104 , PHE A:167 , PRO A:205 , HOH A:746BINDING SITE FOR RESIDUE CL A 501
02AC2SOFTWAREGLY A:37 , THR A:40 , GLN A:102 , GLN A:274BINDING SITE FOR RESIDUE CL A 502
03AC3SOFTWAREASN B:38 , TRP B:104 , PHE B:167 , PRO B:205BINDING SITE FOR RESIDUE CL B 501
04AC4SOFTWAREGLY B:37 , THR B:40 , GLN B:102 , GLN B:274BINDING SITE FOR RESIDUE CL B 502
05AC5SOFTWAREHIS B:277 , PRO B:278 , GLU B:279 , ALA B:280 , HOH B:602 , HOH B:662BINDING SITE FOR RESIDUE ACT B 503
06AC6SOFTWAREASN C:38 , TRP C:104 , PHE C:167 , PRO C:205 , HOH C:724BINDING SITE FOR RESIDUE CL C 501
07AC7SOFTWAREGLY C:37 , THR C:40 , GLN C:102 , GLN C:274BINDING SITE FOR RESIDUE CL C 502
08AC8SOFTWAREASP C:276 , HIS C:277 , PRO C:278 , GLU C:279 , ALA C:280 , HOH C:688 , HOH C:750 , HOH C:769BINDING SITE FOR RESIDUE ACT C 503
09AC9SOFTWAREGLN A:68 , HOH A:676 , HOH A:718 , ILE C:176 , LEU C:177 , HOH C:784BINDING SITE FOR RESIDUE ACT C 504
10BC1SOFTWAREASN D:38 , TRP D:104 , PHE D:167 , PRO D:205BINDING SITE FOR RESIDUE CL D 501
11BC2SOFTWAREGLY D:37 , THR D:40 , GLN D:102 , GLN D:274BINDING SITE FOR RESIDUE CL D 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K2A)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Asn A:38 -Pro A:39
2Glu A:213 -Pro A:214
3Ser A:241 -Pro A:242
4Asn B:38 -Pro B:39
5Glu B:213 -Pro B:214
6Ser B:241 -Pro B:242
7Asn C:38 -Pro C:39
8Glu C:213 -Pro C:214
9Ser C:241 -Pro C:242
10Asn D:38 -Pro D:39
11Glu D:213 -Pro D:214
12Ser D:241 -Pro D:242

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K2A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K2A)

(-) Exons   (0, 0)

(no "Exon" information available for 4K2A)

(-) 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:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..eeeeeeee......eeeee.....hhhhhh.hhhhhh...eeeee...............hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhh..hhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhh....eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k2a A   6 DISLHHRAVLGSTMAYRETGRSDAPHVLFLHGNPTSSYIWRNIMPLVAPVGHCIAPDLIGYGQSGKPDISYRFFDQADYLDALIDELGIASAYLVAQDWGTALAFHLAARRPQLVRGLAFMEFIRPMRDWSDFHQHDAARETFRKFRTPGVGEAMILDNNAFVERVLPGSILRTLSEEEMAAYRAPFATRESRMPTLMLPRELPIAGEPADVTQALTAAHAALAASTYPKLLFVGSPGALVSPAFAAEFAKTLKHCAVIQLGAGGHYLQEDHPEAIGRSVAGWIAGIEAASAQRHA 301
                                    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      


Chain B from PDB  Type:PROTEIN  Length:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..eeeeeeee......eeeee.....hhhhhh.hhhhhh...eeeee...............hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhh..hhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhh...eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k2a B   6 DISLHHRAVLGSTMAYRETGRSDAPHVLFLHGNPTSSYIWRNIMPLVAPVGHCIAPDLIGYGQSGKPDISYRFFDQADYLDALIDELGIASAYLVAQDWGTALAFHLAARRPQLVRGLAFMEFIRPMRDWSDFHQHDAARETFRKFRTPGVGEAMILDNNAFVERVLPGSILRTLSEEEMAAYRAPFATRESRMPTLMLPRELPIAGEPADVTQALTAAHAALAASTYPKLLFVGSPGALVSPAFAAEFAKTLKHCAVIQLGAGGHYLQEDHPEAIGRSVAGWIAGIEAAS 296
                                    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 


Chain C from PDB  Type:PROTEIN  Length:299
                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..eeeeeeee......eeeee.....hhhhhh.hhhhhhhhheeeee...............hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhh..hhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhh...eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k2a C   6 DISLHHRAVLGSTMAYRETGRSDAPHVLFLHGNPTSSYIWRNIMPLVAPVGHCIAPDLIGYGQSGKPDISYRFFDQADYLDALIDELGIASAYLVAQDWGTALAFHLAARRPQLVRGLAFMEFIRPMRDWSDFHQHDAARETFRKFRTPGVGEAMILDNNAFVERVLPGSILRTLSEEEMAAYRAPFATRESRMPTLMLPRELPIAGEPADVTQALTAAHAALAASTYPKLLFVGSPGALVSPAFAAEFAKTLKHCAVIQLGAGGHYLQEDHPEAIGRSVAGWIAGIEAASAQRHAALE 304
                                    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         


Chain D from PDB  Type:PROTEIN  Length:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..eeeeeeee......eeeee.....hhhhhh.hhhhhhhhheeeee...............hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhh..hhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhh...eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k2a D   6 DISLHHRAVLGSTMAYRETGRSDAPHVLFLHGNPTSSYIWRNIMPLVAPVGHCIAPDLIGYGQSGKPDISYRFFDQADYLDALIDELGIASAYLVAQDWGTALAFHLAARRPQLVRGLAFMEFIRPMRDWSDFHQHDAARETFRKFRTPGVGEAMILDNNAFVERVLPGSILRTLSEEEMAAYRAPFATRESRMPTLMLPRELPIAGEPADVTQALTAAHAALAASTYPKLLFVGSPGALVSPAFAAEFAKTLKHCAVIQLGAGGHYLQEDHPEAIGRSVAGWIAGIEAASA 297
                                    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
   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 4K2A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K2A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K2A)

(-) Gene Ontology  (3, 3)

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1cij DHLA FROM XANTHOBACTER AUTOTROPHICUS
1cv2 LINB FROM SPHINGOMONAS PAUCIMOBILIS
2bn6 DHAA FROM RHODOCOCCUS SP
2qvb DMBA FROM MYCOBACTERIUM TUBERCULOSIS
3a2m DBJA FROM BRADYRHIZOBIUM JAPONICUM - USED AS MR MODEL