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(-) Description

Title :  CRYSTAL STRUCTURE OF CORYNEBACTERIUM GLUTAMICUM PIMB' BOUND TO GDP-MAN (ORTHORHOMBIC CRYSTAL FORM)
 
Authors :  S. M. Batt, T. Jabeen, G. S. Besra, K. Futterer
Date :  25 Aug 10  (Deposition) - 15 Sep 10  (Release) - 12 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
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: PET
    Expression System Taxid: 562
    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
1GDD1Ligand/IonGUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE

(-) 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 , TYR A:263 , MET A:266 , GLU A:290 , ILE A:294 , VAL A:295 , GLU A:298 , HOH A:547BINDING SITE FOR RESIDUE GDD A 601

(-) SS Bonds  (0, 0)

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

(-) 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 3OKP)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OKP)

(-) 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_1-3okpA01 A:184-358                                                                                                                                              ----------------------- Pfam domains
         Sec.struct. author ...eeeee.......hhhhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhh....eeeee.......hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhh...eeeee...hhhhhh.hhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhh...eeee.............hhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhh.eeee....hhhhh.....hhhhhhhhhh...eee....hhhhhh....eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3okp 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 3OKP)

(-) CATH Domains  (0, 0)

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

(-) 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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PIMB_CORGL | Q8NNK8: 3oka 3okc

(-) Related Entries Specified in the PDB File

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