Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTALLOGRAPHIC ANALYSIS OF THE POLYSIALIC ACID O-ACETYLTRANSFERASE OATWY
 
Authors :  H. J. Lee, B. Rakic, M. Gilbert, W. W. Wakarchuk, S. G. Withers, N. C. J. S
Date :  23 Jun 09  (Deposition) - 30 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Transferase, Enzyme, Acetyltransferase, Left-Handed Beta Helix (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Lee, B. Rakic, M. Gilbert, W. W. Wakarchuk, S. G. Withers, N. C. J. Strynadka
Structural And Kinetic Characterizations Of The Polysialic Acid O-Acetyltransferase Oatwy From Neisseria Meningitidis.
J. Biol. Chem. V. 284 24501 2009
PubMed-ID: 19525232  |  Reference-DOI: 10.1074/JBC.M109.006049

(-) Compounds

Molecule 1 - POLYSIALIC ACID O-ACETYLTRANSFERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28
    Expression System Strain: DE3
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: NEISSERIA MENINGITIDIS SEROGROUP Y
    Organism Taxid: 648194
    Other Details: LEFT-HANDED BETA HELIX
    Strain: 406Y

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3PO45Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 39)
No.NameCountTypeFull Name
1ACT9Ligand/IonACETATE ION
2EDO15Ligand/Ion1,2-ETHANEDIOL
3PO415Ligand/IonPHOSPHATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:42 , ASP A:63 , ASP A:64 , LYS A:85BINDING SITE FOR RESIDUE ACT A1215
02AC2SOFTWAREHIS A:111 , ASN A:149 , HOH A:2200BINDING SITE FOR RESIDUE ACT A1216
03AC3SOFTWAREHIS A:75 , ALA A:96 , GLU A:97 , HOH A:2051 , HOH A:2111 , HOH A:2202BINDING SITE FOR RESIDUE ACT A1217
04AC4SOFTWAREGLN A:81 , GLN A:83 , SER A:102 , ILE A:103 , GLY A:104 , HOH A:2203 , HOH A:2204BINDING SITE FOR RESIDUE EDO A1218
05AC5SOFTWAREVAL A:189 , LYS A:190 , GLU A:191BINDING SITE FOR RESIDUE EDO A1219
06AC6SOFTWAREHIS A:4 , SER A:7 , GLN A:9 , EDO A:1221 , HOH A:2205 , HOH A:2206BINDING SITE FOR RESIDUE EDO A1220
07AC7SOFTWAREHIS A:4 , GLN A:9 , THR A:19 , EDO A:1220 , HOH A:2017BINDING SITE FOR RESIDUE EDO A1221
08AC8SOFTWAREALA A:110 , MET A:120 , HIS A:121 , ARG A:148 , PO4 A:1223 , HOH A:2208 , HOH A:2209BINDING SITE FOR RESIDUE PO4 A1222
09AC9SOFTWAREARG A:116 , ASP A:119 , MET A:120 , TRP A:145 , GLY A:147 , ARG A:148 , SER A:166 , PO4 A:1222 , EDO A:1227BINDING SITE FOR RESIDUE PO4 A1223
10BC1SOFTWAREGLY A:89 , ASN A:90 , HIS A:111 , HOH A:2209BINDING SITE FOR RESIDUE PO4 A1224
11BC2SOFTWAREASP A:106 , HIS A:143 , ARG A:197 , THR A:209 , LEU A:210 , HOH A:2197 , HOH A:2211BINDING SITE FOR RESIDUE PO4 A1225
12BC3SOFTWAREASN A:56 , ASP A:77 , SER A:202 , ASP A:206 , HOH A:2212 , HOH A:2213BINDING SITE FOR RESIDUE PO4 A1226
13BC4SOFTWARETRP A:145 , GLY A:147 , SER A:166 , PO4 A:1223 , HOH A:2122 , HOH A:2214BINDING SITE FOR RESIDUE EDO A1227

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WLC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WLC)

(-) Exons   (0, 0)

(no "Exon" information available for 2WLC)

(-) 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:211
 aligned with OATWY_NEIME | Q93S40 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:211
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213 
          OATWY_NEIME     4 HMYSEQGINNTINISTTSLTNATQLTVIGNNNSVYIGNNCKIVSSNIRLKGNNITLFIADDVENMGLVCSLHSDCSLQIQAKTTMGNGEITIAEKGKISIGKDCMLAHGYEIRNTDMHPIYSLENGERINHGKDVIIGNHVWLGRNVTILKGVCIPNNVVVGSHTVLYKSFKEPNCVIAGSPAKIVKENIVWGRKMYHSTMYDDPTLNEFY 214
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....eeee.........eeeee....eeee....eee..eeeee....eeee....eee.eeeee....eeee....ee..eeeee....eeee....ee...eeee.....................eee....ee....ee....ee....ee....ee........eeee....eeeee...........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wlc A   4 HMYSEQGINNTINISTTSLTNATQLTVIGNNNSVYIGNNCKIVSSNIRLKGNNITLFIADDVEIMGLVCSLHSDCSLQIQAKTTMGNGEITIAEKGKISIGKDCMLAHGYEIRNTDMHPIYSLENGERINHGKDVIIGNHVWLGRNVTILKGVCIPNNVVVGSHTVLYKSFKEPNCVIAGSPAKIVKENIVWGRKMYHSTMYDDPTLNEFY 214
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213
   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 2WLC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2WLC)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (OATWY_NEIME | Q93S40)
molecular function
    GO:0050208    polysialic-acid O-acetyltransferase activity    Catalysis of the reaction: acetyl-CoA + an alpha-2,8-linked polymer of sialic acid = CoA + polysialic acid acetylated at O-7 or O-9.
    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.
biological process
    GO:0070207    protein homotrimerization    The formation of a protein homotrimer, a macromolecular structure consisting of three noncovalently associated identical subunits.

 Visualization

(-) Interactive Views

Asymmetric 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2wlc)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  2wlc
    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
  OATWY_NEIME | Q93S40
    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)
  (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
  OATWY_NEIME | Q93S40
    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
        OATWY_NEIME | Q93S40: 2wld 2wle 2wlf 2wlg

(-) Related Entries Specified in the PDB File

2wld CRYSTALLOGRAPHIC ANALYSIS OF THE POLYSIALIC ACID O-ACETYLTRANSFERASE OATWY
2wle CRYSTALLOGRAPHIC ANALYSIS OF THE POLYSIALIC ACID O-ACETYLTRANSFERASE OATWY
2wlf CRYSTALLOGRAPHIC ANALYSIS OF THE POLYSIALIC ACID O-ACETYLTRANSFERASE OATWY
2wlg CRYSTALLOGRAPHIC ANALYSIS OF THE POLYSIALIC ACID O-ACETYLTRANSFERASE OATWY