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(-) Description

Title :  SULFATE BOUND L-HALOACID DEHALOGENASE FROM A RHODOBACTERACEAE FAMILY BACTERIUM
 
Authors :  H. R. Novak, C. Sayer, M. N. Isupov, K. Paszkiewicz, D. Gotz, A. M. Spragg J. A. Littlechild
Date :  09 Oct 12  (Deposition) - 01 May 13  (Release) - 25 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C,D  (1x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. R. Novak, C. Sayer, M. N. Isupov, K. Paszkiewicz, D. Gotz, A. Mearns Spragg, J. A. Littlechild
Marine Rhodobacteraceae L-Haloacid Dehalogenase Contains A Novel His/Glu Dyad That Could Activate The Catalytic Water.
Febs J. V. 280 1664 2013
PubMed-ID: 23384397  |  Reference-DOI: 10.1111/FEBS.12177

(-) Compounds

Molecule 1 - L-HALOACID DEHALOGENASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: RIPL
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Organism Scientific: RHODOBACTERACEAE
    Organism Taxid: 31989

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):   CD
Biological Unit 2 (1x): AB  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:18 , VAL A:19 , ASN A:20 , THR A:124 , ASN A:125 , LYS A:157BINDING SITE FOR RESIDUE SO4 A1237
2AC2SOFTWAREASP B:18 , VAL B:19 , ASN B:20 , THR B:124 , ASN B:125 , LYS B:157BINDING SITE FOR RESIDUE SO4 B1237
3AC3SOFTWAREASP C:18 , VAL C:19 , ASN C:20 , THR C:124 , ASN C:125 , LYS C:157BINDING SITE FOR RESIDUE SO4 C1237
4AC4SOFTWAREASP D:18 , VAL D:19 , ASN D:20 , THR D:124 , ASN D:125 , LYS D:157BINDING SITE FOR RESIDUE SO4 D1237

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YMM)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric 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
5Ala C:131 -Pro C:132
6Lys C:157 -Pro C:158
7Ala D:131 -Pro D:132
8Lys D:157 -Pro D:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YMM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YMM)

(-) Exons   (0, 0)

(no "Exon" information available for 2YMM)

(-) 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:225
 aligned with R4GRT2_9RHOB | R4GRT2 from UniProtKB/TrEMBL  Length:236

    Alignment length:225
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231     
         R4GRT2_9RHOB    12 SGILVFDVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACHIWDTIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASLTA 236
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...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
                 2ymm A  12 SGILVFDVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACHIWDTIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASLTA 236
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231     


Chain B from PDB  Type:PROTEIN  Length:228
 aligned with R4GRT2_9RHOB | R4GRT2 from UniProtKB/TrEMBL  Length:236

    Alignment length:228
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228        
         R4GRT2_9RHOB     9 PSRSGILVFDVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACHIWDTIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASLTA 236
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhhh..eeeeee........hhhhhh.hhhhh.eeee.........hhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhh...eeeee.................eee.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ymm B   9 PSRSGILVFDVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACHIWDTIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASLTA 236
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228        


Chain C from PDB  Type:PROTEIN  Length:225
 aligned with R4GRT2_9RHOB | R4GRT2 from UniProtKB/TrEMBL  Length:236

    Alignment length:225
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231     
         R4GRT2_9RHOB    12 SGILVFDVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACHIWDTIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASLTA 236
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhhh..eeeeee........hhhhhh.hhhhh.eeee.hhh.....hhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhh...eeeee.................eee.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ymm C  12 SGILVFDVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACHIWDTIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASLTA 236
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231     


Chain D from PDB  Type:PROTEIN  Length:225
 aligned with R4GRT2_9RHOB | R4GRT2 from UniProtKB/TrEMBL  Length:236

    Alignment length:225
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231     
         R4GRT2_9RHOB    12 SGILVFDVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACHIWDTIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASLTA 236
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhhh..eeeeee........hhhhhh.hhhhh.eeee.hhh.....hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhh...eeeee.................eee.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ymm D  12 SGILVFDVNETLLDLTSLSPLFERVFGDAKVLREWFPELILYSQTLTLTGLYRPFGEIAAAVFEMVAANHQAKVTPDDIAELKTRLTSMPAYPDVAPALTRLQDAGFRLVTLTNSAPSPAPSPLEKAGIASFFEAHLTVHSSQRFKPHPSVYDSTAETLGAKPEELCMIACHIWDTIGAQARGWRGGFVARPHNTPLTLAEVPQPDFIGRDMGELADQLIASLTA 236
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 2YMM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YMM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YMM)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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.

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 Related Entries

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

UniProtKB/TrEMBL
        R4GRT2_9RHOB | R4GRT2: 2yml 2ymp 2ymq 2yn4 4ce6 4cf3 4cf4 4cf5 4cnq

(-) Related Entries Specified in the PDB File

2yml NATIVE L-HALOACID DEHALOGENASE FROM A RHODOBACTERACEAE FAMILY BACTERIUM
2ymp CHLOROACETIC ACID COMPLEX BOUND L-HALOACID DEHALOGENASE FROM A RHODOBACTERACEAE FAMILY BACTERIUM
2ymq CHLOROPROPIONIC ACID COMPLEX BOUND L-HALOACID DEHALOGENASE FROM A RHODOBACTERACEAE FAMILY BACTERIUM
2yn4 L-2-CHLOROBUTRYIC ACID BOUND COMPLEX L-HALOACID DEHALOGENASE FROM A RHODOBACTERACEAE FAMILY BACTERIUM