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(-) Description

Title :  CRYSTAL STRUCTURE OF DL-2-HALOACID DEHALOGENASE
 
Authors :  A. Siwek, R. Omi, K. Hirotsu, K. Jitsumori, N. Esaki, T. Kurihara, P. Pan
Date :  06 Oct 13  (Deposition) - 27 Nov 13  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,D,E,F,G
Keywords :  Dehalogenases, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Siwek, R. Omi, K. Hirotsu, K. Jitsumori, N. Esaki, T. Kurihara, P. Paneth
Binding Modes Of Dl-2-Haloacid Dehalogenase Revealed By Crystallography, Modeling And Isotope Effects Studies.
Arch. Biochem. Biophys. V. 540 26 2013
PubMed-ID: 24071515  |  Reference-DOI: 10.1016/J.ABB.2013.09.012

(-) Compounds

Molecule 1 - DL-2-HALOACID DEHALOGENASE
    Chains: A, B, D, E, F, G
    EC Number: 3.8.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DL-DEX
    Organism Scientific: METHYLOBACTERIUM
    Organism Taxid: 439332
    Strain: CPA1

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABDEFG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric/Biological Unit (1, 12)
No.NameCountTypeFull Name
1GOL12Ligand/IonGLYCEROL

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:15 , ALA A:23 , ASP A:27 , HIS A:30 , LYS A:162 , HOH A:639 , HOH A:738 , HOH A:892 , HOH A:922BINDING SITE FOR RESIDUE GOL A 401
02AC2SOFTWAREARG A:210 , PRO A:215 , HOH A:573 , HOH A:602 , HOH A:604 , HOH A:752 , HOH A:802 , HOH A:843 , HOH A:907 , LEU D:74BINDING SITE FOR RESIDUE GOL A 402
03AC3SOFTWAREHIS B:15 , ALA B:23 , ASP B:27 , HIS B:30 , LYS B:162 , HOH B:744 , HOH B:837 , HOH B:865 , HOH B:901BINDING SITE FOR RESIDUE GOL B 401
04AC4SOFTWAREARG B:210 , PRO B:215 , HOH B:538 , HOH B:555 , HOH B:577 , HOH B:668 , HOH B:689 , HOH B:957 , LEU G:74 , HOH G:733BINDING SITE FOR RESIDUE GOL B 402
05AC5SOFTWAREHIS D:15 , ALA D:23 , ASP D:27 , HIS D:30 , LYS D:162 , HOH D:636 , HOH D:872 , HOH D:918 , HOH D:935BINDING SITE FOR RESIDUE GOL D 401
06AC6SOFTWAREARG D:210 , PRO D:215 , HOH D:602 , HOH D:895 , HOH D:913 , HOH D:951 , HOH D:966 , HOH D:974 , LEU F:74BINDING SITE FOR RESIDUE GOL D 402
07AC7SOFTWAREHIS E:15 , ALA E:23 , ASP E:27 , HIS E:30 , LYS E:162 , HOH E:877 , HOH E:932 , HOH E:964 , HOH E:974BINDING SITE FOR RESIDUE GOL E 401
08AC8SOFTWARELEU B:74 , ARG E:210 , PRO E:215 , HOH E:578 , HOH E:599 , HOH E:638 , HOH E:780 , HOH E:968 , HOH E:985BINDING SITE FOR RESIDUE GOL E 402
09AC9SOFTWAREHIS F:15 , ALA F:23 , ASP F:27 , HIS F:30 , LYS F:162 , HOH F:726 , HOH F:759 , HOH F:815BINDING SITE FOR RESIDUE GOL F 401
10BC1SOFTWARELEU A:74 , HOH A:736 , ARG F:210 , PRO F:215 , HOH F:612 , HOH F:780 , HOH F:909 , HOH F:929 , HOH F:931 , HOH F:965BINDING SITE FOR RESIDUE GOL F 402
11BC2SOFTWAREHIS G:15 , ALA G:23 , ASP G:27 , HIS G:30 , LYS G:162 , HOH G:678 , HOH G:878 , HOH G:904 , HOH G:925BINDING SITE FOR RESIDUE GOL G 401
12BC3SOFTWARELEU E:74 , ARG G:210 , PRO G:215 , HOH G:580 , HOH G:588 , HOH G:629 , HOH G:797 , HOH G:823 , HOH G:956BINDING SITE FOR RESIDUE GOL G 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N2X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4N2X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N2X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N2X)

(-) Exons   (0, 0)

(no "Exon" information available for 4N2X)

(-) 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
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhh....hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh................hhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh........hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n2x A   4 RSVLGSFPQVDHHQAKGQLAEVYDDIHNTMRVPWVAFGIRVMSQFPHFIPDAWAALKPNIETRYAEDGADLIRLNSIVPGPVMPNPTPKLLRLGWTESKIEELKTALDLLNYGNPKYLILITAFNEAWHERDTGGRAPQKLRGRDAERIPYGLPNSVEKFNLLDIEKASDRTQTVLRDIRDAFLHHGPASDYRVLGVWPDYLEIALRDSLAPVALSAEYDETARRIRKIAREHVKGFDKPAGVAWRDMTEKLSAEQIAGLTGLLFMYNRFIADITIAIIRLKQAFSGPEDATANKYTN 301
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293        


Chain B from PDB  Type:PROTEIN  Length:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhh....hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh.....................hhhhhhhhhhhhhhh.....hhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh........hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n2x B   4 RSVLGSFPQVDHHQAKGQLAEVYDDIHNTMRVPWVAFGIRVMSQFPHFIPDAWAALKPNIETRYAEDGADLIRLNSIVPGPVMPNPTPKLLRLGWTESKIEELKTALDLLNYGNPKYLILITAFNEAWHERDTGGRAPQKLRGRDAERIPYGLPNSVEKFNLLDIEKASDRTQTVLRDIRDAFLHHGPASDYRVLGVWPDYLEIALRDSLAPVALSAEYDETARRIRKIAREHVKGFDKPAGVAWRDMTEKLSAEQIAGLTGLLFMYNRFIADITIAIIRLKQAFSGPEDATANKYTN 301
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293        


Chain D from PDB  Type:PROTEIN  Length:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhh....hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh................hhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh........hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n2x D   4 RSVLGSFPQVDHHQAKGQLAEVYDDIHNTMRVPWVAFGIRVMSQFPHFIPDAWAALKPNIETRYAEDGADLIRLNSIVPGPVMPNPTPKLLRLGWTESKIEELKTALDLLNYGNPKYLILITAFNEAWHERDTGGRAPQKLRGRDAERIPYGLPNSVEKFNLLDIEKASDRTQTVLRDIRDAFLHHGPASDYRVLGVWPDYLEIALRDSLAPVALSAEYDETARRIRKIAREHVKGFDKPAGVAWRDMTEKLSAEQIAGLTGLLFMYNRFIADITIAIIRLKQAFSGPEDATANKYTN 301
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293        


Chain E from PDB  Type:PROTEIN  Length:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhh....hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh................hhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh........hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n2x E   4 RSVLGSFPQVDHHQAKGQLAEVYDDIHNTMRVPWVAFGIRVMSQFPHFIPDAWAALKPNIETRYAEDGADLIRLNSIVPGPVMPNPTPKLLRLGWTESKIEELKTALDLLNYGNPKYLILITAFNEAWHERDTGGRAPQKLRGRDAERIPYGLPNSVEKFNLLDIEKASDRTQTVLRDIRDAFLHHGPASDYRVLGVWPDYLEIALRDSLAPVALSAEYDETARRIRKIAREHVKGFDKPAGVAWRDMTEKLSAEQIAGLTGLLFMYNRFIADITIAIIRLKQAFSGPEDATANKYTN 301
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293        


Chain F from PDB  Type:PROTEIN  Length:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhh....hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh.....................hhhhhhhhhhhhhhh.....hhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh........hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n2x F   4 RSVLGSFPQVDHHQAKGQLAEVYDDIHNTMRVPWVAFGIRVMSQFPHFIPDAWAALKPNIETRYAEDGADLIRLNSIVPGPVMPNPTPKLLRLGWTESKIEELKTALDLLNYGNPKYLILITAFNEAWHERDTGGRAPQKLRGRDAERIPYGLPNSVEKFNLLDIEKASDRTQTVLRDIRDAFLHHGPASDYRVLGVWPDYLEIALRDSLAPVALSAEYDETARRIRKIAREHVKGFDKPAGVAWRDMTEKLSAEQIAGLTGLLFMYNRFIADITIAIIRLKQAFSGPEDATANKYTN 301
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293        


Chain G from PDB  Type:PROTEIN  Length:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhh....hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh................hhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh........hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n2x G   4 RSVLGSFPQVDHHQAKGQLAEVYDDIHNTMRVPWVAFGIRVMSQFPHFIPDAWAALKPNIETRYAEDGADLIRLNSIVPGPVMPNPTPKLLRLGWTESKIEELKTALDLLNYGNPKYLILITAFNEAWHERDTGGRAPQKLRGRDAERIPYGLPNSVEKFNLLDIEKASDRTQTVLRDIRDAFLHHGPASDYRVLGVWPDYLEIALRDSLAPVALSAEYDETARRIRKIAREHVKGFDKPAGVAWRDMTEKLSAEQIAGLTGLLFMYNRFIADITIAIIRLKQAFSGPEDATANKYTN 301
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293
   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 4N2X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N2X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N2X)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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        A6BM74_9RHIZ | A6BM74: 3wj8

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