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(-) Description

Title :  STRUCTURE FROM THE MOBILE METAGENOME OF V. PSEUDOCHOLERAE. VPC_CASS1
 
Authors :  S. J. Harrop, C. N. Deshpande, V. Sureshan, Y. Boucher, X. Xu, H. Cui, C. Chang, A. Edwards, A. Joachimiak, A. Savchenko, P. M. G. Curmi, B. C. Mabbutt, Midwest Center For Structural Genomics (Mcsg)
Date :  20 Oct 08  (Deposition) - 13 Jan 09  (Release) - 12 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Integron Cassette Protein, Dioxygenase, Oxidoreductase, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Harrop, C. N. Deshpande, V. Sureshan, Y. Boucher, X. Xu, H. Cui, C. Chang, A. Edwards, A. Joachimiak, A. Savchenko, P. M. G. Curmi, B. C. Mabbutt
Structure From The Mobile Metagenome Of V. Pseudocholerae. Vpc_cass1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE III-RELATED PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TV LIC
    Expression System Strain: BL21-CODONPLUS(DE3)-RIPL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: VC_A0328, VC_A0341, VC_A0463
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:104 , THR A:105 , HOH A:155 , HOH A:190 , HOH A:210 , HOH A:280BINDING SITE FOR RESIDUE SO4 A 133
2AC2SOFTWARETHR A:16 , HIS A:55 , LEU A:57 , GLY A:58 , HIS A:59 , LYS A:64 , VAL A:68 , HOH A:267 , HOH B:233BINDING SITE FOR RESIDUE SO4 A 134

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EY8)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu A:62 -Pro A:63
2Gly A:100 -Pro A:101
3Glu B:62 -Pro B:63
4Gly B:100 -Pro B:101

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EY8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EY8)

(-) Exons   (0, 0)

(no "Exon" information available for 3EY8)

(-) 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:129
 aligned with Q9K3D3_VIBCH | Q9K3D3 from UniProtKB/TrEMBL  Length:132

    Alignment length:129
                                    12        22        32        42        52        62        72        82        92       102       112       122         
         Q9K3D3_VIBCH     3 FLMKISHLDHLVLTVADIPTTTNFYEKVLGMKAVSFGAGRIALEFGHQKINLHQLGNEFEPKAQNVRVGSADLCFITDTVLSDAMKHVENQGVTIMEGPVKRTGAQGAITSFYFRDPDGNLIEVSTYSN 131
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------3ey8A01 A:11-131 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee.hhhhhhhhhhhhhh.eeeee...eeeeee..eeeeeee.................eeeee...hhhhhhhhhhhh.....eeeeeeee..eeeeeeeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ey8 A   3 FLmKISHLDHLVLTVADIPTTTKFYEKVLGmKAVSFGSGRIALEFGHQKINLHQLGHEFEPKAQNVRTGSADLCFITDIDLSDAmEYVENQGVVImEGPVKRTGAQGAITSFYFRDPDGNLIEVSTYSN 131
                              |     12        22        32|       42        52        62        72        82    |   92     | 102       112       122         
                              |                          33-MSE                                                87-MSE     98-MSE                             
                              5-MSE                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:131
 aligned with Q9K3D3_VIBCH | Q9K3D3 from UniProtKB/TrEMBL  Length:132

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
         Q9K3D3_VIBCH     1 MEFLMKISHLDHLVLTVADIPTTTNFYEKVLGMKAVSFGAGRIALEFGHQKINLHQLGNEFEPKAQNVRVGSADLCFITDTVLSDAMKHVENQGVTIMEGPVKRTGAQGAITSFYFRDPDGNLIEVSTYSN 131
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------3ey8B01 B:11-131 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeee.hhhhhhhhhhhhhh.eeeee...eeeeee..eeeeeee.................eeeee...hhhhhhhhhhhh.....eeeeeeee..eeeeeeeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ey8 B   1 mEFLmKISHLDHLVLTVADIPTTTKFYEKVLGmKAVSFGSGRIALEFGHQKINLHQLGHEFEPKAQNVRTGSADLCFITDIDLSDAmEYVENQGVVImEGPVKRTGAQGAITSFYFRDPDGNLIEVSTYSN 131
                            |   |   10        20        30  |     40        50        60        70        80      | 90       100       110       120       130 
                            1-MSE                          33-MSE                                                87-MSE     98-MSE                             
                                5-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  (0, 0)

(no "SCOP Domain" information available for 3EY8)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EY8)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9K3D3_VIBCH | Q9K3D3)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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.
biological process
    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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 Related Entries

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

UniProtKB/TrEMBL
        Q9K3D3_VIBCH | Q9K3D3: 3ey7

(-) Related Entries Specified in the PDB File

3ey7 RELATED ID: APC7783 RELATED DB: TARGETDB