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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE ECTOINE HYDROXYLASE ECTD FROM SALIBACILLUS SALEXIGENS
 
Authors :  K. Reuter, A. Heine
Date :  25 Sep 08  (Deposition) - 29 Sep 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Double Stranded Beta Helix, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Reuter, M. Pittelkow, J. Bursy, A. Heine, T. Craan, E. Bremer
Synthesis Of 5-Hydroxyectoine From Ectoine: Crystal Structure Of The Non-Heme Iron(Ii) And 2-Oxoglutarate-Dependent Dioxygenase Ectd
Plos One V. 5 E1064 2010
PubMed-ID: 20498719  |  Reference-DOI: 10.1371/JOURNAL.PONE.0010647

(-) Compounds

Molecule 1 - ECTD
    Chains: A
    EC Number: 1.14.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PASK-IBA3
    Expression System Strain: DH5ALPHA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ECTD
    Organism Common: SALIBACILLUS SALEXIGENS
    Organism Scientific: VIRGIBACILLUS SALEXIGENS
    Organism Taxid: 61016
    Strain: DSM-11483
    Synonym: ECTOINE HYDROXYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1FE1Ligand/IonFE (III) ION
2GOL2Ligand/IonGLYCEROL
3MSE7Mod. Amino AcidSELENOMETHIONINE
4SO44Ligand/IonSULFATE ION
Biological Unit 1 (3, 13)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2GOL2Ligand/IonGLYCEROL
3MSE7Mod. Amino AcidSELENOMETHIONINE
4SO44Ligand/IonSULFATE ION
Biological Unit 2 (3, 26)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2GOL4Ligand/IonGLYCEROL
3MSE14Mod. Amino AcidSELENOMETHIONINE
4SO48Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:146 , ASP A:148 , HIS A:248 , HOH A:823 , HOH A:824 , HOH A:851BINDING SITE FOR RESIDUE FE A 400
2AC2SOFTWAREGLY A:122 , ARG A:162BINDING SITE FOR RESIDUE SO4 A 601
3AC3SOFTWAREPRO A:136 , GLY A:137 , ARG A:220 , PRO A:256 , PRO A:258 , HOH A:864 , HOH A:886BINDING SITE FOR RESIDUE SO4 A 602
4AC4SOFTWAREARG A:220 , ARG A:224 , HOH A:857 , HOH A:898BINDING SITE FOR RESIDUE SO4 A 603
5AC5SOFTWAREARG A:92 , LYS A:139 , GLY A:140 , LYS A:141BINDING SITE FOR RESIDUE SO4 A 604
6AC6SOFTWAREPRO A:34 , PHE A:54 , ARG A:112 , HOH A:749 , HOH A:815BINDING SITE FOR RESIDUE GOL A 701
7AC7SOFTWARESER A:167 , ASN A:173 , PRO A:179 , LEU A:180 , HOH A:733 , HOH A:775BINDING SITE FOR RESIDUE GOL A 702

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3EMR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3EMR)

(-) 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:279
 aligned with ECTD_VIRSA | Q2TDY4 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:296
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290      
           ECTD_VIRSA     1 MEDLYPSRQNNQPKILKRKDPVIYTDRSKDNQAPITKEQLDSYEKNGFLQIKNFFSEDEVIDMQKAIFELQDSIKDVASDKVIREPESNDIRSIFHVHQDDNYFQDVANDKRILDIVRHLLGSDVYVHQSRINYKPGFKGKEFDWHSDFETWHVEDGMPRMRAISVSIALSDNYSFNGPLMLIPGSHNYFVSCVGETPDNNYKESLKKQKLGVPDEESLRELTRIGGGISVPTGKAGSVTLFESNTMHGSTSNITPYPRNNLFMVYNSVKNRLVEPFSGGEKRPEYIAVREKQPVY 296
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeee........hhhhhhhh..hhhhhhhhhhhheeee....hhhhhhhhhhhhhhhhhhh.......eee......eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee.........eeeehhhhhhhhhhh.....eeeeeee...........ee..hhh.eeee..-----------------...hhhhhhhhhhhhh...........eeeee....eee..........eeeeeeee.hhh........................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3emr A   1 mEDLYPSRQNNQPKILKRKDPVIYTDRSKDNQAPITKEQLDSYEKNGFLQIKNFFSEDEVIDmQKAIFELQDSIKDVASDKVIREPESNDIRSIFHVHQDDNYFQDVANDKRILDIVRHLLGSDVYVHQSRINYKPGFKGKEFDWHSDFETWHVEDGmPRmRAISVSIALSDNYSFNGPLmLIPGSHNYFVSCV-----------------GVPDEESLRELTRIGGGISVPTGKAGSVTLFESNTmHGSTSNITPYPRNNLFmVYNSVKNRLVEPFSGGEKRPEYIAVREKQPVY 296
                            |       10        20        30        40        50        60  |     70        80        90       100       110       120       130       140       150       160|      170       180|      190   |     -         - |     220       230       240      |250       260   |   270       280       290      
                            |                                                            63-MSE                                                                                        158-MSE                181-MSE      194               212                                247-MSE          264-MSE                            
                            1-MSE                                                                                                                                                         161-MSE
   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 3EMR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3EMR)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (ECTD_VIRSA | Q2TDY4)
molecular function
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016706    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors    Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor.
biological process
    GO:0019491    ectoine biosynthetic process    The chemical reactions and pathways resulting in the formation of ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid), a tetrahydropyrimidine commonly synthesized by halophilic bacteria.
    GO:0042400    ectoine catabolic process    The chemical reactions and pathways resulting in the breakdown of ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid), a tetrahydropyrimidine commonly synthesized by halophilic bacteria.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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        ECTD_VIRSA | Q2TDY4: 4nmi

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