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(-) Description

Title :  STRUCTURE OF AN ESTERASE FROM THE OIL-DEGRADING BACTERIUM OLEISPIRA ANTARCTICA
 
Authors :  A. U. Singer, E. Evdokimova, O. Kagan, A. M. Edwards, A. Joachimiak, A. S Midwest Center For Structural Genomics (Mcsg)
Date :  07 Jul 09  (Deposition) - 28 Jul 09  (Release) - 09 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oleispira Antarctica, Lipase, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Lemak, A. Tchigvintsev, P. Petit, R. Flick, A. U. Singer, G. Brown, E. Evdokimova, O. Egorova, C. F. Gonzalez, T. N. Chernikova, M. M. Yakimov, M. Kube, R. Reinhardt, P. N. Golyshin, A. Savchenko, A. F. Yakunin
Structure And Activity Of The Cold-Active And Anion-Activated Carboxyl Esterase Olei01171 From The Oil-Degrading Marine Bacterium Oleispira Antarctica.
Biochem. J. V. 445 193 2012
PubMed-ID: 22519667  |  Reference-DOI: 10.1042/BJ20112113

(-) Compounds

Molecule 1 - ESTERASE APC40077
    Chains: A, B
    EC Number: 3.1.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TV LIC
    Expression System Strain: BL21(DE3)-RIPL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: OLEI01171
    Organism Scientific: OLEISPIRA ANTARCTICA
    Organism Taxid: 188908

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 21)

Asymmetric Unit (4, 21)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO6Ligand/Ion1,2-ETHANEDIOL
3MSE12Mod. Amino AcidSELENOMETHIONINE
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3MSE6Mod. Amino AcidSELENOMETHIONINE
4PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (3, 9)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3MSE6Mod. Amino AcidSELENOMETHIONINE
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:55 , SER A:148 , MSE A:149 , HOH A:299BINDING SITE FOR RESIDUE CL A 280
2AC2SOFTWAREVAL A:22 , SER A:23 , ASN A:24 , ASN A:27 , CYS A:28 , HOH A:541BINDING SITE FOR RESIDUE EDO A 281
3AC3SOFTWARELYS A:65 , TYR A:259 , TYR A:260 , HOH A:336 , GLN B:64 , HOH B:290BINDING SITE FOR RESIDUE EDO A 282
4AC4SOFTWAREALA A:223 , ASN A:225 , ASP A:256 , HOH A:313 , HOH A:375 , HOH A:423 , HOH B:358BINDING SITE FOR RESIDUE EDO A 283
5AC5SOFTWAREPRO A:181 , LYS A:185 , HOH A:432 , HOH A:516BINDING SITE FOR RESIDUE EDO A 284
6AC6SOFTWARELEU B:55 , SER B:148 , MSE B:149 , HOH B:317BINDING SITE FOR RESIDUE CL B 280
7AC7SOFTWARELYS B:10 , GLY B:13 , HOH B:387BINDING SITE FOR RESIDUE EDO B 281
8AC8SOFTWARESER B:58 , ASP B:59 , ASP B:83 , ARG B:87 , HOH B:398 , HOH B:450 , HOH B:532BINDING SITE FOR RESIDUE EDO B 282
9AC9SOFTWAREMSE A:63 , GLN A:64 , LYS B:65 , TYR B:259 , TYR B:260 , HOH B:292 , HOH B:336 , HOH B:407 , HOH B:485BINDING SITE FOR RESIDUE PEG B 283

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3I6Y)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:112 -Pro A:113
2Ala B:112 -Pro B:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3I6Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3I6Y)

(-) Exons   (0, 0)

(no "Exon" information available for 3I6Y)

(-) 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:278
 aligned with D0VWZ4_OLEAN | D0VWZ4 from UniProtKB/TrEMBL  Length:280

    Alignment length:278
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272        
         D0VWZ4_OLEAN     3 SIENLSSNKSFGGWHKQYSHVSNTLNCAMRFAIYLPPQASTGAKVPVLYWLSGLTCSDENFMQKAGAQRLAAELGIAIVAPDTSPRGEGVADDEGYDLGQGAGFYVNATQAPWNRHYQMYDYVVNELPELIESMFPVSDKRAIAGHSMGGHGALTIALRNPERYQSVSAFSPINNPVNCPWGQKAFTAYLGKDTDTWREYDASLLMRAAKQYVPALVDQGEADNFLAEQLKPEVLEAAASSNNYPLELRSHEGYDHSYYFIASFIEDHLRFHSNYLNA 280
               SCOP domains d3i6ya_ A: automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3i6yA00 A:2-279  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..eeeeeeeeee....eeeeeeeeehhhhhh...eeeeeee.......hhhhhhh.hhhhhhhhh.eeeee..............................hhhhh.hhhhhhhhhhhhhhhhhh.eeeeeeeeeehhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i6y A   2 SIENLSSNKSFGGWHKQYSHVSNTLNCAmRFAIYLPPQASTGAKVPVLYWLSGLTCSDENFmQKAGAQRLAAELGIAIVAPDTSPRGEGVADDEGYDLGQGAGFYVNATQAPWNRHYQmYDYVVNELPELIESmFPVSDKRAIAGHSmGGHGALTIALRNPERYQSVSAFSPINNPVNCPWGQKAFTAYLGKDTDTWREYDASLLmRAAKQYVPALVDQGEADNFLAEQLKPEVLEAAASSNNYPLELRSHEGYDHSYYFIASFIEDHLRFHSNYLNA 279
                                    11        21        31        41        51        61 |      71        81        91       101       111       121       131   |   141       151       161       171       181       191       201     | 211       221       231       241       251       261       271        
                                                       30-MSE                           63-MSE                                                  120-MSE        135-MSE       149-MSE                                                   207-MSE                                                                    


Chain B from PDB  Type:PROTEIN  Length:278
 aligned with D0VWZ4_OLEAN | D0VWZ4 from UniProtKB/TrEMBL  Length:280

    Alignment length:278
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272        
         D0VWZ4_OLEAN     3 SIENLSSNKSFGGWHKQYSHVSNTLNCAMRFAIYLPPQASTGAKVPVLYWLSGLTCSDENFMQKAGAQRLAAELGIAIVAPDTSPRGEGVADDEGYDLGQGAGFYVNATQAPWNRHYQMYDYVVNELPELIESMFPVSDKRAIAGHSMGGHGALTIALRNPERYQSVSAFSPINNPVNCPWGQKAFTAYLGKDTDTWREYDASLLMRAAKQYVPALVDQGEADNFLAEQLKPEVLEAAASSNNYPLELRSHEGYDHSYYFIASFIEDHLRFHSNYLNA 280
               SCOP domains d3i6yb_ B: automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3i6yB00 B:2-279  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..eeeeeeeeee....eeeeeeeeehhhhhh...eeeeeee.......hhhhhhh.hhhhhhhhh.eeeee..............................hhhhh.hhhhhhhhhhhhhhhhhh.eeeeeeeeeehhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i6y B   2 SIENLSSNKSFGGWHKQYSHVSNTLNCAmRFAIYLPPQASTGAKVPVLYWLSGLTCSDENFmQKAGAQRLAAELGIAIVAPDTSPRGEGVADDEGYDLGQGAGFYVNATQAPWNRHYQmYDYVVNELPELIESmFPVSDKRAIAGHSmGGHGALTIALRNPERYQSVSAFSPINNPVNCPWGQKAFTAYLGKDTDTWREYDASLLmRAAKQYVPALVDQGEADNFLAEQLKPEVLEAAASSNNYPLELRSHEGYDHSYYFIASFIEDHLRFHSNYLNA 279
                                    11        21        31        41        51        61 |      71        81        91       101       111       121       131   |   141       151       161       171       181       191       201     | 211       221       231       241       251       261       271        
                                                       30-MSE                           63-MSE                                                  120-MSE        135-MSE       149-MSE                                                   207-MSE
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3I6Y)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (D0VWZ4_OLEAN | D0VWZ4)
molecular function
    GO:0018738    S-formylglutathione hydrolase activity    Catalysis of the reaction: S-formylglutathione + H(2)O = formate + glutathione + H(+).
    GO:0052689    carboxylic ester hydrolase activity    Catalysis of the hydrolysis of a carboxylic ester bond.
    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.
biological process
    GO:0046294    formaldehyde catabolic process    The chemical reactions and pathways resulting in the breakdown of formaldehyde (methanal, H2C=O), the simplest aldehyde.

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