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 :  STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF THE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE FROM CLOSTRIDIUM PERFRINGENS
 
Authors :  M. C. Pelissier, C. Sebban-Kreuzer, F. Guerlesquin, J. A. Brannigan, G. J. Davies, Y. Bourne, F. Vincent
Date :  23 Jul 14  (Deposition) - 15 Oct 14  (Release) - 14 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Isomerase, Sugar 2-Epimerase, Sialic Acid, Sugar Phosphate, Enzyme Mechanism, Carbohydrate, Mutagenesis, 1H Nmr Spectroscopy (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Pelissier, C. Sebban-Kreuzer, F. Guerlesquin, J. A. Brannigan, G. J. Davies, Y. Bourne, F. Vincent
Structural And Functional Characterization Of The Clostridium Perfringens N-Acetylmannosamine-6-Phosphate 2-Epimerase Essential For The Sialic Acid Salvage Pathway
J. Biol. Chem. V. 289 35215 2014
PubMed-ID: 25320079  |  Reference-DOI: 10.1074/JBC.M114.604272

(-) Compounds

Molecule 1 - N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
    Chains: A, B
    EC Number: 5.1.3.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-YSBLIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA
    Organism Scientific: CLOSTRIDIUM PERFRINGENS STR. 13
    Organism Taxid: 195102
    Other Details: N-ACETYLMANNOSAMINE-6-PHOSPHATE BOUND TO MOLECULE A AND B
    Synonym: MANNAC-6-P EPIMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2LRY2Ligand/IonN-ACETYLMANNOSAMINE-6-PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:14 , ARG A:43 , TYR A:75 , THR A:147 , TYR A:151 , GLU A:180 , GLY A:181 , ARG A:182 , GLY A:203 , GLY A:204 , ARG A:208 , HOH A:2055 , HOH A:2058 , HOH A:2198 , HOH A:2202 , HOH A:2235 , HOH A:2236 , HOH A:2256 , HOH A:2261 , HOH A:2274 , HOH A:2275BINDING SITE FOR RESIDUE LRY A 301
2AC2SOFTWAREGLN B:14 , ARG B:43 , ILE B:64 , TYR B:75 , THR B:147 , TYR B:151 , GLU B:180 , GLY B:181 , ARG B:182 , GLY B:203 , GLY B:204 , ARG B:208 , HOH B:2030 , HOH B:2033 , HOH B:2161 , HOH B:2165 , HOH B:2185 , HOH B:2186 , HOH B:2202 , HOH B:2210 , HOH B:2222 , HOH B:2223BINDING SITE FOR RESIDUE LRY B 301
3AC3SOFTWAREARG A:208 , PRO A:209 , GLN A:210 , HOH A:2069 , HOH A:2070BINDING SITE FOR RESIDUE CL A1221
4AC4SOFTWAREARG B:208 , PRO B:209 , GLN B:210 , HOH B:2045 , HOH B:2049BINDING SITE FOR RESIDUE CL B1221

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4UTU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4UTU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UTU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UTU)

(-) Exons   (0, 0)

(no "Exon" information available for 4UTU)

(-) 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:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhh..eeee..........hhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhh..eeee..............hhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eee................hhhhhhhhhhhh...eeee....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4utu A  -8 GSSHHHHHHMLDVVKGNLIVSCQALSDEPLHSSFIMGRMAIAAKQGGAAAIRAQGVNDINEIKEVTKLPIIGIIARNYDDSEIYITPTMKEVDELLKTDCEMIALDATKRKRPNGENVKDLVDAIHAKGRLAMADISTLEEGIEAEKLGFDCVSTTLSGYTPYSKQSNSVDFELLEELVKTVKIPVICEGRINTPEELKKALDLGAYSAVVGGAITRPQQITKRFTDIL 220
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         


Chain B from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhh..eeee..........hhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhh..eeee..............hhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eee................hhhhhhhhhh.....eeee....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4utu B  -8 GSSHHHHHHMLDVVKGNLIVSCQALSDEPLHSSFIMGRMAIAAKQGGAAAIRAQGVNDINEIKEVTKLPIIGIIARNYDDSEIYITPTMKEVDELLKTDCEMIALDATKRKRPNGENVKDLVDAIHAKGRLAMADISTLEEGIEAEKLGFDCVSTTLSGYTPYSKQSNSVDFELLEELVKTVKIPVICEGRINTPEELKKALDLGAYSAVVGGAITRPQQITKRFTDIL 220
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
   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 4UTU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UTU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UTU)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    LRY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4utu)
 

(-) 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
  4utu
    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
  NANE_CLOPE | Q8XNZ3
    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)
  5.1.3.9
    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
  NANE_CLOPE | Q8XNZ3
    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
        NANE_CLOPE | Q8XNZ3: 4utw

(-) Related Entries Specified in the PDB File

4utt STRUCTURAL CHARACTERISATION OF NANE, MANNAC6P C2 EPIMERASE, FROM CLOSTRIDIUM PERFINGENS
4utw STRUCTURAL CHARACTERISATION OF NANE, MANNAC6P C2 EPIMERASE, FROM CLOSTRIDIUM PERFINGENS