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 :  CRYSTAL STRUCTURE OF PROTEIN GI:16801725, MEMBER OF ENOLASE SUPERFAMILY FROM LISTERIA INNOCUA CLIP11262
 
Authors :  A. A. Fedorov, E. V. Fedorov, W. S. Yew, J. A. Gerlt, S. C. Almo, S. K. Burle York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  07 Dec 04  (Deposition) - 21 Dec 04  (Release) - 24 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Unknown Function, Nysgxrc Target T2186, Enolase Superfamily, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Odokonyero, A. Sakai, Y. Patskovsky, V. N. Malashkevich, A. A. Fedorov, J. B. Bonanno, E. V. Fedorov, R. Toro, R. Agarwal, C. Wang N. D. Ozerova, W. S. Yew, J. M. Sauder, S. Swaminathan, S. K. Burley, S. C. Almo, M. E. Glasner
Loss Of Quaternary Structure Is Associated With Rapid Sequence Divergence In The Osbs Family
Proc. Natl. Acad. Sci. Usa V. 111 8535 2014
PubMed-ID: 24872444  |  Reference-DOI: 10.1073/PNAS.1318703111

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN LIN2664
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: LISTERIA INNOCUA
    Organism Taxid: 272626
    Strain: CLIP11262

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:1214 , ASP A:1239 , GLU A:1240BINDING SITE FOR RESIDUE MG A 5001
2AC2SOFTWAREGLU B:2214 , ASP B:2239 , GLU B:2240BINDING SITE FOR RESIDUE MG B 5002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WUF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WUF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WUF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WUF)

(-) Exons   (0, 0)

(no "Exon" information available for 1WUF)

(-) 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:371
 aligned with Q927X3_LISIN | Q927X3 from UniProtKB/TrEMBL  Length:374

    Alignment length:371
                             1                                                                                                                                                                                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369 
        Q927X3_LISIN      - -MYFQKARLIHAELPLLAPFKTSYGELKSKDFYIIELINEEGIHGYGELEAFPLPDYTEETLSSAILIIKEQLLPLLAQRKIRKPEEIQELFSWIQGNEMAKAAVELAVWDAFAKMEKRSLAKMIGATKESIKVGVSIGLQQNVETLLQLVNQYVDQGYERVKLKIAPNKDIQFVEAVRKSFPKLSLMADANSAYNREDFLLLKELDQYDLEMIEQPFGTKDFVDHAWLQKQLKTRICLDENIRSVKDVEQAHSIGSCRAINLKLARVGGMSSALKIAEYCALNEILVWCGGMLEAGVGRAHNIALAARNEFVFPGDISASNRFFAEDIVTPAFELNQGRLKVPTNEGIGVTLDLKVLKKYTKSTEEILLN  370
               SCOP domains -d1wufa2 A:1001-1126 N-acylamino acid racemase                                                                                 d1wufa1 A:1127-1370 N-acylamino acid racemase                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------1wufA02 A:1118-1361 Enolase superfamily                                                                                                                                                                                                             --------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..eeeeeeeeeeeeeeeee..eeeeeeeeeeeeee.....eeeeee...........hhhhhhhhhhhhhhhhhhhhee...hhhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhh.....eee..eee....hhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhh..eee.......hhhhhhhhh....eeee.....hhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh...........hhhhh...............eee...........hhhhhhh.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wuf A 1000 HMYFQKARLIHAELPLLAPFKTSYGELKSKDFYIIELINEEGIHGYGELEAFPLPDYTEETLSSAILIIKEQLLPLLAQRKIRKPEEIQELFSWIQGNEMAKAAVELAVWDAFAKMEKRSLAKMIGATKESIKVGVSIGLQQNVETLLQLVNQYVDQGYERVKLKIAPNKDIQFVEAVRKSFPKLSLMADANSAYNREDFLLLKELDQYDLEMIEQPFGTKDFVDHAWLQKQLKTRICLDENIRSVKDVEQAHSIGSCRAINLKLARVGGMSSALKIAEYCALNEILVWCGGMLEAGVGRAHNIALAARNEFVFPGDISASNRFFAEDIVTPAFELNQGRLKVPTNEGIGVTLDLKVLKKYTKSTEEILLN 1370
                                  1009      1019      1029      1039      1049      1059      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189      1199      1209      1219      1229      1239      1249      1259      1269      1279      1289      1299      1309      1319      1329      1339      1349      1359      1369 


Chain B from PDB  Type:PROTEIN  Length:371
 aligned with Q927X3_LISIN | Q927X3 from UniProtKB/TrEMBL  Length:374

    Alignment length:371
                             1                                                                                                                                                                                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369 
        Q927X3_LISIN      - -MYFQKARLIHAELPLLAPFKTSYGELKSKDFYIIELINEEGIHGYGELEAFPLPDYTEETLSSAILIIKEQLLPLLAQRKIRKPEEIQELFSWIQGNEMAKAAVELAVWDAFAKMEKRSLAKMIGATKESIKVGVSIGLQQNVETLLQLVNQYVDQGYERVKLKIAPNKDIQFVEAVRKSFPKLSLMADANSAYNREDFLLLKELDQYDLEMIEQPFGTKDFVDHAWLQKQLKTRICLDENIRSVKDVEQAHSIGSCRAINLKLARVGGMSSALKIAEYCALNEILVWCGGMLEAGVGRAHNIALAARNEFVFPGDISASNRFFAEDIVTPAFELNQGRLKVPTNEGIGVTLDLKVLKKYTKSTEEILLN  370
               SCOP domains -d1wufb2 B:2001-2126 N-acylamino acid racemase                                                                                 d1wufb1 B:2127-2370 N-acylamino acid racemase                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------1wufB02 B:2118-2361 Enolase superfamily                                                                                                                                                                                                             --------- CATH domains
           Pfam domains (1) ----MR_MLE_N-1wufB01 B:2004-2125                                                                                              -----------------------------------------------------------------------------------------------------------------MR_MLE_C-1wufB03 B:2239-2351                                                                                     ------------------- Pfam domains (1)
           Pfam domains (2) ----MR_MLE_N-1wufB02 B:2004-2125                                                                                              -----------------------------------------------------------------------------------------------------------------MR_MLE_C-1wufB04 B:2239-2351                                                                                     ------------------- Pfam domains (2)
         Sec.struct. author .ee..eeeeeeeeeeeeeeeee..eeeeeeeeeeeeee.....eeeeee...........hhhhhhhhhhhhhhhhhhhhee...hhhhhhh.....hhhhhhhhhhhhhhhhhhhh..hhhhhh.....eee..eee....hhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhh.....eeeee.....hhhhhhhhhhhhh....eee.......hhhhhhhhh....eeee.....hhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh...........hhhhh...............eee...........hhhhhhh.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wuf B 2000 HMYFQKARLIHAELPLLAPFKTSYGELKSKDFYIIELINEEGIHGYGELEAFPLPDYTEETLSSAILIIKEQLLPLLAQRKIRKPEEIQELFSWIQGNEMAKAAVELAVWDAFAKMEKRSLAKMIGATKESIKVGVSIGLQQNVETLLQLVNQYVDQGYERVKLKIAPNKDIQFVEAVRKSFPKLSLMADANSAYNREDFLLLKELDQYDLEMIEQPFGTKDFVDHAWLQKQLKTRICLDENIRSVKDVEQAHSIGSCRAINLKLARVGGMSSALKIAEYCALNEILVWCGGMLEAGVGRAHNIALAARNEFVFPGDISASNRFFAEDIVTPAFELNQGRLKVPTNEGIGVTLDLKVLKKYTKSTEEILLN 2370
                                  2009      2019      2029      2039      2049      2059      2069      2079      2089      2099      2109      2119      2129      2139      2149      2159      2169      2179      2189      2199      2209      2219      2229      2239      2249      2259      2269      2279      2289      2299      2309      2319      2329      2339      2349      2359      2369
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Enolase_N (69)
(-)
Family: MR_MLE_N (47)
(-)
Listeria innocua (1)
1aMR_MLE_N-1wufB01B:2004-2125
1bMR_MLE_N-1wufB02B:2004-2125
(-)
Clan: Enolase_TIM (82)
(-)
Family: MR_MLE_C (29)
(-)
Listeria innocua (1)
2aMR_MLE_C-1wufB03B:2239-2351
2bMR_MLE_C-1wufB04B:2239-2351

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q927X3_LISIN | Q927X3)
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:0016836    hydro-lyase activity    Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0009234    menaquinone biosynthetic process    The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.
    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.

 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
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1wuf)
 

(-) 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
  1wuf
    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
  Q927X3_LISIN | Q927X3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  Q927X3_LISIN | Q927X3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1WUF)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1WUF)