Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  PUTATIVE THIOSULFATE SULFURTRANSFERASE YNJE
 
Authors :  J. P. Declercq, A. Smeets, M. Depuydt, J. F. Collet
Date :  25 Jun 09  (Deposition) - 01 Sep 10  (Release) - 05 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Rhodanese Domains (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Declercq, A. Smeets, M. Depuydt, J. F. Collet
Structural Analysis Of Ynje, A Putative Thiosulfate Sulfurtransferase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE THIOSULFATE SULFURTRANSFERASE YNJE
    Chains: A
    EC Number: 2.8.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PET3A
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: SE-MET DERIVATIVE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric/Biological Unit (3, 13)
No.NameCountTypeFull Name
1CSD1Mod. Amino Acid3-SULFINOALANINE
2EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:155 , GLU A:178 , TRP A:183 , LYS A:265 , TYR A:308 , THR A:367 , TRP A:369 , HOH A:2272 , HOH A:2302 , HOH A:2432 , HOH A:2546 , HOH A:2547BINDING SITE FOR RESIDUE EPE A1412
2AC2SOFTWAREGLN A:14 , GLN A:18 , TRP A:296 , TRP A:320 , TRP A:353 , HOH A:2548 , HOH A:2549 , HOH A:2550BINDING SITE FOR RESIDUE EPE A1413

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:180 -Pro A:181
2Ile A:266 -Pro A:267

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 5)

Asymmetric/Biological Unit (3, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RHODANESE_3PS50206 Rhodanese domain profile.YNJE_ECOLI36-138
164-270
304-425		  3A:16-118
A:144-250
A:284-405
2RHODANESE_1PS00380 Rhodanese signature 1.YNJE_ECOLI181-192  1A:161-172
3RHODANESE_2PS00683 Rhodanese C-terminal signature.YNJE_ECOLI406-416  1A:386-396

(-) Exons   (0, 0)

(no "Exon" information available for 2WLR)

(-) 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:408
 aligned with YNJE_ECOLI | P78067 from UniProtKB/Swiss-Prot  Length:435

    Alignment length:408
                                    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       303       313       323       333       343       353       363       373       383       393       403       413       423        
           YNJE_ECOLI    24 AELAKPLTLDQLQQQNGKAIDTRPSAFYNGWPQTLNGPSGHELAALNLSASWLDKMSTEQLNAWIKQHNLKTDAPVALYGNDKDVDAVKTRLQKAGLTHISILSDALSEPSRLQKLPHFEQLVYPQWLHDLQQGKEVTAKPAGDWKVIEAAWGAPKLYLISHIPGADYIDTNEVESEPLWNKVSDEQLKAMLAKHGIRHDTTVILYGRDVYAAARVAQIMLYAGVKDVRLLDGGWQTWSDAGLPVERGTPPKVKAEPDFGVKIPAQPQLMLDMEQARGLLHRQDASLVSIRSWPEFIGTTSGYSYIKPKGEIAGARWGHAGSDSTHMEDFHNPDGTMRSADDITAMWKAWNIKPEQQVSFYCGTGWRASETFMYARAMGWKNVSVYDGGWYEWSSDPKNPVATGERGP 431
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Rhodanese-2wlrA01 A:275-399                                                                                                  ------------ Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Rhodanese-2wlrA02 A:275-399                                                                                                  ------------ Pfam domains (2)
         Sec.struct. author .......hhhhhhhh..eeee..hhhhhhh...............ee.hhhhhhhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhh....eee......hhhhh....hhh.eehhhhhhhhhh...........eeeeeee....hhhhhh.....eeee....ee....ee.hhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhhhh...eeee..hhhhhhhh........................hhh.eehhhhhhh......eeeee..hhhhhh.............ee...ee.........hhhh........hhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhh....eeee.hhhhhhh......ee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ------------RHODANESE_3  PDB: A:16-118 UniProt: 36-138                                                             -------------------------RHODANESE_3  PDB: A:144-250 UniProt: 164-270                                                               ---------------------------------RHODANESE_3  PDB: A:284-405 UniProt: 304-425                                                                              ------ PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------RHODANESE_1 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RHODANESE_2--------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wlr A   4 AELAKPLTLDQLQQQNGKAIDTRPSAFYNGWPQTLNGPSGHELAALNLSASWLDKmSTEQLNAWIKQHNLKTDAPVALYGNDKDVDAVKTRLQKAGLTHISILSDALSEPSRLQKLPHFEQLVYPQWLHDLQQGKEVTAKPAGDWKVIEAAWGAPKLYLISHIPGADYIDTNEVESEPLWNKVSDEQLKAmLAKHGIRHDTTVILYGRDVYAAARVAQImLYAGVKDVRLLDGGWQTWSDAGLPVERGTPPKVKAEPDFGVKIPAQPQLmLDmEQARGLLHRQDASLVSIRSWPEFIGTTSGYSYIKPKGEIAGARWGHAGSDSTHmEDFHNPDGTmRSADDITAmWKAWNIKPEQQVSFYcGTGWRASETFmYARAmGWKNVSVYDGGWYEWSSDPKNPVATGERGP 411
                                    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       303       313       323      |333      |343     | 353       363 |     373  |    383       393       403        
                                                                                  59-MSE                                                                                                                                194-MSE                      223-MSE                                           273-MSE                                                  330-MSE   340-MSE  349-MSE         365-CSD    376-MSE|                              
                                                                                                                                                                                                                                                                                                          276-MSE                                                                                                  381-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 2WLR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Rhodanese] (33)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (YNJE_ECOLI | P78067)
molecular function
    GO:0016783    sulfurtransferase activity    Catalysis of the transfer of sulfur atoms from one compound (donor) to another (acceptor).
    GO:0004792    thiosulfate sulfurtransferase activity    Catalysis of the reaction: hydrogen cyanide + thiosulfate = H(+) + sulfite + thiocyanate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CSD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EPE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:180 - Pro A:181   [ RasMol ]  
    Ile A:266 - Pro A:267   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2wlr
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  YNJE_ECOLI | P78067
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.8.1.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  YNJE_ECOLI | P78067
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        YNJE_ECOLI | P78067: 2wlx 3ipo 3ipp

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2WLR)