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(-) Description

Title :  CRYSTAL STRUCTURE OF CORYNEBACTERIUM GLUTAMICUM PIMB' IN COMPLEX WITH GDP-MAN (TRICLINIC 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 :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Gt-B Fold, Alpha-Mannosyltransferase, Gdp-Man Binding, 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, B
    EC Number: 2.4.1.57
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET16B
    Expression System Taxid: 562
    Expression System Vector Type: PET
    Gene: PIMB, CGL2186, CG2400
    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
 
Molecule 2 - N-TERMINAL HIS-AFFINITY TAG
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: HIS-AFFINITY TAG
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1GDD2Ligand/IonGUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
2GOL1Ligand/IonGLYCEROL
3SO410Ligand/IonSULFATE ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1GDD1Ligand/IonGUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
2GOL1Ligand/IonGLYCEROL
3SO44Ligand/IonSULFATE ION
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1GDD1Ligand/IonGUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
2GOL-1Ligand/IonGLYCEROL
3SO46Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:206 , ARG A:210 , ARG A:239 , HOH A:387 , HOH A:437 , HIS D:-19BINDING SITE FOR RESIDUE SO4 A 601
02AC2SOFTWARELYS A:54 , PRO A:209 , ARG A:239 , ARG A:283 , HOH A:451 , HIS D:-19BINDING SITE FOR RESIDUE SO4 A 602
03AC3SOFTWAREPRO A:128 , GLY A:129 , SER A:130 , ARG A:131 , GLN A:132BINDING SITE FOR RESIDUE SO4 A 603
04AC4SOFTWAREARG A:206 , ARG A:210 , LYS A:211 , VAL A:235 , GLY A:236 , ARG A:260 , LEU A:261 , MET A:266 , GLU A:298 , HOH A:533 , HOH A:536BINDING SITE FOR RESIDUE GDD A 701
05AC5SOFTWARETHR A:71 , THR A:73 , GLU A:360 , HOH A:535BINDING SITE FOR RESIDUE GOL A 801
06AC6SOFTWAREARG B:206 , ARG B:210 , ARG B:239 , HOH B:389BINDING SITE FOR RESIDUE SO4 B 601
07AC7SOFTWARELYS B:54 , ARG B:239 , ARG B:283BINDING SITE FOR RESIDUE SO4 B 602
08AC8SOFTWAREPRO B:128 , GLY B:129 , SER B:130 , ARG B:131 , GLN B:132BINDING SITE FOR RESIDUE SO4 B 603
09AC9SOFTWAREHIS B:50 , LYS B:54 , HIS C:-17 , HIS C:-18BINDING SITE FOR RESIDUE SO4 B 604
10BC1SOFTWAREARG B:206 , LYS B:211 , VAL B:235 , GLY B:236 , ARG B:260 , LEU B:261 , TYR B:263 , MET B:266 , GLU B:298 , HOH B:507 , HOH B:510BINDING SITE FOR RESIDUE GDD B 701
11BC2SOFTWAREHIS C:-15 , HIS C:-14 , HIS C:-16BINDING SITE FOR RESIDUE SO4 C 700
12BC3SOFTWAREHIS A:50 , LYS A:54 , HIS D:-17 , HIS D:-19 , HIS D:-18BINDING SITE FOR RESIDUE SO4 D 702
13BC4SOFTWAREHIS D:-14 , HIS D:-15 , HIS D:-16BINDING SITE FOR RESIDUE SO4 D 701

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Pro A:15 -Pro A:16
2Ala A:96 -Pro A:97
3Pro B:15 -Pro B:16
4Ala B:96 -Pro B:97

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OKA)

(-) 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: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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee.......hhhhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhh....eeeee.......hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhh...eeeee............hhhhhhhhhhhhh.eeee.hhhhhhhhh.......eeee.............hhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhh.eeee....hhhhh.....hhhhhhhhhh...eeee...hhhhhh....eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3oka 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        


Chain B 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 (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Glycos_transf_1-3okaB01 B:184-358                                                                                                                                              ----------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Glycos_transf_1-3okaB02 B:184-358                                                                                                                                              ----------------------- Pfam domains (2)
         Sec.struct. author ...eeeee.......hhhhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhh...eeeee............hhhhhhhhhhhhh.eeee.hhhhhhhhh.......eeee.............hhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh.eeeee..hhhhhhhhhhh..eeee....hhhhh.....hhhhhhhhhh...eeee...hhhhhh....eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3oka B   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        


Chain C from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 3oka C -18 HHHHHHSSGHI  -8
                                    -9 


Chain D from PDB  Type:PROTEIN  Length:14
                                              
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .............. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                 3oka D -20 HHHHHHHHSSGHIE  -7
                                   -11
   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 3OKA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: GT-B (132)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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  2.4.1.57
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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