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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL GLOBULAR DOMAIN OF OLIGOSACCHARYLTRANSFERASE (AFAGLB-S2, AF_0040, O30195_ARCFU) FROM ARCHAEOGLOBUS FULGIDUS
 
Authors :  J. Nyirenda, S. Matsumoto, T. Saitoh, N. Maita, N. N. Noda, F. Inagaki, D
Date :  13 Jun 12  (Deposition) - 23 Jan 13  (Release) - 23 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Glycotransferase, Asn-Glycosylation, Membrane, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Nyirenda, S. Matsumoto, T. Saitoh, N. Maita, N. N. Noda, F. Inagaki, D. Kohda
Crystallographic And Nmr Evidence For Flexibility In Oligosaccharyltransferases And Its Catalytic Significance
Structure V. 21 32 2013
PubMed-ID: 23177926  |  Reference-DOI: 10.1016/J.STR.2012.10.011

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: A, B, C
    EC Number: 2.4.1.119
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-41B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL GLOBULAR DOMAIN
    Gene: AGLB
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 224325
    Strain: DSM 4304
    Synonym: OLIGOSACCHARYLTRANSFERASE AGLB

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 27)

Asymmetric Unit (2, 27)
No.NameCountTypeFull Name
1MES3Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 9)
No.NameCountTypeFull Name
1MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:440 , GLU A:530 , THR A:531 , LYS A:582 , ASN A:583BINDING SITE FOR RESIDUE MES A 601
2AC2SOFTWAREGLU B:440 , PRO B:529 , GLU B:530 , ASN B:532 , LYS B:582 , ASN B:583BINDING SITE FOR RESIDUE MES B 601
3AC3SOFTWAREGLU C:440 , PRO C:529 , GLU C:530 , THR C:531 , ASN C:532 , LYS C:582 , ASN C:583BINDING SITE FOR RESIDUE MES C 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VU0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VU0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VU0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VU0)

(-) Exons   (0, 0)

(no "Exon" information available for 3VU0)

(-) 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:153
 aligned with O30195_ARCFU | O30195 from UniProtKB/TrEMBL  Length:593

    Alignment length:162
                                   441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591  
         O30195_ARCFU   432 VEMTMDWKEALNWMKENLEAQDYLKAYEKPDYAVLSWWDYGNWILYVAKKAVVCNNFQAGADDAAKFFTAQSEEEAMKIVEKRKVRYVVTVEELTVKPETNKTKFIPIMQIAGYSPEYMKNKEIIDFFNKTMLYKLHVENATNLTHFRLLKNFGTVKIFEVK 593
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh...---------..eee.hhhhhhhhhhh............hhhhhhhhhhh.hhhhhhhhhhhhheeeeeee.hhh........hhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhh........eeeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vu0 A 432 mEmTmDWKEALNWmKENLEAQ---------DYAVLSWWDYGNWILYVAKKAVVCNNFQAGADDAAKFFTAQSEEEAmKIVEKRKVRYVVTVEELTVKPETNKTKFIPImQIAGYSPEYmKNKEIIDFFNKTmLYKLHVENATNLTHFRLLKNFGTVKIFEVK 593
                            | | |  441   |   451|        -|      471       481       491       501      |511       521       531       541       551       561 |     571       581       591  
                            | | |      445-MSE452       462                                           508-MSE                         540-MSE   550-MSE      563-MSE                          
                          432-MSE                                                                                                                                                             
                            434-MSE                                                                                                                                                           
                              436-MSE                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:162
 aligned with O30195_ARCFU | O30195 from UniProtKB/TrEMBL  Length:593

    Alignment length:162
                                   441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591  
         O30195_ARCFU   432 VEMTMDWKEALNWMKENLEAQDYLKAYEKPDYAVLSWWDYGNWILYVAKKAVVCNNFQAGADDAAKFFTAQSEEEAMKIVEKRKVRYVVTVEELTVKPETNKTKFIPIMQIAGYSPEYMKNKEIIDFFNKTMLYKLHVENATNLTHFRLLKNFGTVKIFEVK 593
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh..............eee.hhhhhhhhhhh............hhhhhhhhhhh.hhhhhhhhhhhhheeeeeee.hhh........hhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhh........eeeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vu0 B 432 mEmTmDWKEALNWmKENLEAQDYLKAYEKPDYAVLSWWDYGNWILYVAKKAVVCNNFQAGADDAAKFFTAQSEEEAmKIVEKRKVRYVVTVEELTVKPETNKTKFIPImQIAGYSPEYmKNKEIIDFFNKTmLYKLHVENATNLTHFRLLKNFGTVKIFEVK 593
                            | | |  441   |   451       461       471       481       491       501      |511       521       531       541       551       561 |     571       581       591  
                          432-MSE      445-MSE                                                        508-MSE                         540-MSE   550-MSE      563-MSE                          
                            434-MSE                                                                                                                                                           
                              436-MSE                                                                                                                                                         


Chain C from PDB  Type:PROTEIN  Length:154
 aligned with O30195_ARCFU | O30195 from UniProtKB/TrEMBL  Length:593

    Alignment length:162
                                   441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591  
         O30195_ARCFU   432 VEMTMDWKEALNWMKENLEAQDYLKAYEKPDYAVLSWWDYGNWILYVAKKAVVCNNFQAGADDAAKFFTAQSEEEAMKIVEKRKVRYVVTVEELTVKPETNKTKFIPIMQIAGYSPEYMKNKEIIDFFNKTMLYKLHVENATNLTHFRLLKNFGTVKIFEVK 593
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh...--------...eee.hhhhhhhhhhh............hhhhhhhhhhh.hhhhhhhhhhhh.eeeeeee.hhh........hhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhh........eeeeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vu0 C 432 mEmTmDWKEALNWmKENLEAQ--------PDYAVLSWWDYGNWILYVAKKAVVCNNFQAGADDAAKFFTAQSEEEAmKIVEKRKVRYVVTVEELTVKPETNKTKFIPImQIAGYSPEYmKNKEIIDFFNKTmLYKLHVENATNLTHFRLLKNFGTVKIFEVK 593
                            | | |  441   |   451|      461       471       481       491       501      |511       521       531       541       551       561 |     571       581       591  
                          432-MSE      445-MSE452      461                                            508-MSE                         540-MSE   550-MSE      563-MSE                          
                            434-MSE                                                                                                                                                           
                              436-MSE
   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 3VU0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VU0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VU0)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (O30195_ARCFU | O30195)
molecular function
    GO:0004576    oligosaccharyl transferase activity    Catalysis of the transfer of a oligosaccharyl group to an acceptor molecule, typically another carbohydrate or a lipid.
biological process
    GO:0006486    protein glycosylation    A protein modification process that results in the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid, e.g. the addition of glycan chains to proteins.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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3vu1