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 CORYNEBACTERIUM GLUTAMICUM PIMB' BOUND TO GDP (ORTHORHOMBIC CRYSTAL FORM)
 
Authors :  S. M. Batt, T. Jabeen, G. S. Besra, K. Futterer
Date :  24 Aug 10  (Deposition) - 15 Sep 10  (Release) - 12 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Gt-B Fold, Alpha-Mannosyltransferase, Gdp-Man, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Batt, T. Jabeen, A. K. Mishra, N. Veerapen, K. Krumbach, L. Eggeling, G. S. Besra, K. Futterer
Acceptor Substrate Discrimination In Phosphatidyl-Myo-Inositol Mannoside Synthesis: Structural And Mutational Analysis Of Mannosyltransferase Corynebacterium Glutamicum Pimb'.
J. Biol. Chem. V. 285 37741 2010
PubMed-ID: 20843801  |  Reference-DOI: 10.1074/JBC.M110.165407

(-) Compounds

Molecule 1 - GDP-MANNOSE-DEPENDENT ALPHA-(1-6)-PHOSPHATIDYLINOSITOL MONOMANNOSIDE MANNOSYLTRANSFERASE
    Chains: A
    EC Number: 2.4.1.57
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PET
    Gene: CG2400, CGL2186, NCGL2106, PIMB
    Organism Common: BREVIBACTERIUM FLAVUM
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM
    Organism Taxid: 1718
    Synonym: GUANOSINE DIPHOSPHOMANNOSE-PHOSPHATIDYL-INOSITOL ALPHA- MANNOSYLTRANSFERASE, PHOSPHATIDYLINOSITOL ALPHA-MANNOSYLTRANSFERASE, PI ALPHA-MANNOSYLTRANSFERASE, ALPHA-MANNOSYLTRANSFERASE, ALPHA-MANT, ALPHA-D-MANNOSE-ALPHA-(1-6)-PHOSPHATIDYLMYO-INOSITOL- MANNOSYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:206 , ARG A:210 , LYS A:211 , VAL A:235 , GLY A:236 , ARG A:260 , LEU A:261 , MET A:266 , ILE A:294 , VAL A:295 , GLU A:298 , HOH A:468BINDING SITE FOR RESIDUE GDP A 601

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:15 -Pro A:16
2Ala A:96 -Pro A:97

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OKC)

(-) 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:378
 aligned with PIMB_CORGL | Q8NNK8 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:378
                                    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        
           PIMB_CORGL     4 SRKTLVVTNDFPPRIGGIQSYLRDFIATQDPESIVVFASTQNAEEAHAYDKTLDYEVIRWPRSVMLPTPTTAHAMAEIIREREIDNVWFGAAAPLALMAGTAKQAGASKVIASTHGHEVGWSMLPGSRQSLRKIGTEVDVLTYISQYTLRRFKSAFGSHPTFEHLPSGVDVKRFTPATPEDKSATRKKLGFTDTTPVIACNSRLVPRKGQDSLIKAMPQVIAARPDAQLLIVGSGRYESTLRRLATDVSQNVKFLGRLEYQDMINTLAAADIFAMPARTRGGGLDVEGLGIVYLEAQACGVPVIAGTSGGAPETVTPATGLVVEGSDVDKLSELLIELLDDPIRRAAMGAAGRAHVEAEWSWEIMGERLTNILQSEPR 381
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Glycos_transf_1-3okcA01 A:184-358                                                                                                                                              ----------------------- Pfam domains
         Sec.struct. author ...eeeee.......hhhhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhh....eeeee.......hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh..eeeee..hhhhhhh.hhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhh...eeee.............hhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhh.eeee....hhhhh.....hhhhhhhhhh...eeee...hhhhhh....eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3okc A   4 SRKTLVVTNDFPPRIGGIQSYLRDFIATQDPESIVVFASTQNAEEAHAYDKTLDYEVIRWPRSVMLPTPTTAHAMAEIIREREIDNVWFGAAAPLALMAGTAKQAGASKVIASTHGHEVGWSMLPGSRQSLRKIGTEVDVLTYISQYTLRRFKSAFGSHPTFEHLPSGVDVKRFTPATPEDKSATRKKLGFTDTTPVIACNSRLVPRKGQDSLIKAMPQVIAARPDAQLLIVGSGRYESTLRRLATDVSQNVKFLGRLEYQDMINTLAAADIFAMPARTRGGGLDVEGLGIVYLEAQACGVPVIAGTSGGAPETVTPATGLVVEGSDVDKLSELLIELLDDPIRRAAMGAAGRAHVEAEWSWEIMGERLTNILQSEPR 381
                                    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
   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 3OKC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OKC)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: GT-B (132)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PIMB_CORGL | Q8NNK8)
molecular function
    GO:0033164    glycolipid 6-alpha-mannosyltransferase activity    Catalysis of the transfer of an alpha-D-mannosyl residue from GDP-mannose into lipid-linked oligosaccharide, forming an alpha-(1->6)-D-mannosyl-D-mannose linkage.
    GO:0043750    phosphatidylinositol alpha-mannosyltransferase activity    Catalysis of the transfer of one or more alpha-D-mannose residues from GDP-mannose to positions 2,6 and others in 1-phosphatidyl-myo-inositol.
    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.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0009247    glycolipid biosynthetic process    The chemical reactions and pathways resulting in the formation of glycolipid, a class of 1,2-di-O-acylglycerols joined at oxygen 3 by a glycosidic linkage to a carbohydrate part (usually a mono-, di- or tri-saccharide).
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0097502    mannosylation    The covalent attachment of a mannose residue to a substrate molecule.
    GO:0046488    phosphatidylinositol metabolic process    The chemical reactions and pathways involving phosphatidylinositol, any glycophospholipid in which a sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
    GO:0008654    phospholipid biosynthetic process    The chemical reactions and pathways resulting in the formation of phospholipids, any lipid containing phosphoric acid as a mono- or diester.

 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
    GDP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:96 - Pro A:97   [ RasMol ]  
    Pro A:15 - Pro A:16   [ 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
  3okc
    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
  PIMB_CORGL | Q8NNK8
    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)
  2.4.1.57
    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
  PIMB_CORGL | Q8NNK8
    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
        PIMB_CORGL | Q8NNK8: 3oka 3okp

(-) Related Entries Specified in the PDB File

3oka PIMB' BOUND TO GDP-MAN (TRICLINNIC CRYSTAL FORM)
3okp PIMB' BOUND TO GDP-MAN (ORTHORHOMBIC CRYSTAL FORM)