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(-) Description

Title :  CRYSTAL STRUCTURE OF CLASS I ALPHA-1,2-MANNOSIDASE FROM SACCHAROMYCES CEREVISIAE AT 1.54 ANGSTROM RESOLUTION
 
Authors :  F. Vallee, F. Lipari, P. Yip, A. Herscovics, P. L. Howell
Date :  08 Dec 99  (Deposition) - 18 Feb 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.54
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Alpha Helix Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Vallee, F. Lipari, P. Yip, B. Sleno, A. Herscovics, P. L. Howell
Crystal Structure Of A Class I Alpha1, 2-Mannosidase Involve In N-Glycan Processing And Endoplasmic Reticulum Quality Control.
Embo J. V. 19 581 2000
PubMed-ID: 10675327  |  Reference-DOI: 10.1093/EMBOJ/19.4.581

(-) Compounds

Molecule 1 - CLASS I ALPHA-1,2-MANNOSIDASE
    Chains: A
    EC Number: 3.2.1.113
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: YPH33
    Expression System Taxid: 4922
    Expression System Vector: PHIL-S1
    Fragment: CATALYTIC DOMAIN
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 13)

Asymmetric/Biological Unit (6, 13)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2CA1Ligand/IonCALCIUM ION
3GOL1Ligand/IonGLYCEROL
4MAN4Ligand/IonALPHA-D-MANNOSE
5NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
6NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:93 , ASN A:96 , LEU A:151 , NDG A:601 , HOH A:969 , HOH A:1133BINDING SITE FOR RESIDUE NAG A 600
02AC2SOFTWAREARG A:273 , GLU A:515 , NAG A:600 , BMA A:602 , MAN A:603 , MAN A:606BINDING SITE FOR RESIDUE NDG A 601
03AC3SOFTWAREARG A:273 , NDG A:601 , MAN A:603 , MAN A:604 , HOH A:1082 , HOH A:1181 , HOH A:1186BINDING SITE FOR RESIDUE BMA A 602
04AC4SOFTWAREARG A:273 , ARG A:433 , NDG A:601 , BMA A:602 , MAN A:605 , MAN A:606 , HOH A:1089BINDING SITE FOR RESIDUE MAN A 603
05AC5SOFTWAREASN A:129 , SER A:185 , ASN A:196 , BMA A:602 , HOH A:1081BINDING SITE FOR RESIDUE MAN A 604
06AC6SOFTWAREPHE A:131 , GLU A:207 , SER A:272 , ARG A:273 , ASP A:275 , MAN A:603 , HOH A:1083 , HOH A:1095 , HOH A:1189BINDING SITE FOR RESIDUE MAN A 605
07AC7SOFTWAREARG A:269 , SER A:272 , ASP A:336 , LEU A:338 , GLU A:399 , NDG A:601 , MAN A:603 , HOH A:985 , HOH A:1147 , HOH A:1148 , HOH A:1150BINDING SITE FOR RESIDUE MAN A 606
08AC8SOFTWAREASP A:168 , ASN A:224 , THR A:226 , NAG A:801 , HOH A:934 , HOH A:1192 , HOH A:1193 , HOH A:1195 , HOH A:1256BINDING SITE FOR RESIDUE NAG A 800
09AC9SOFTWAREALA A:171 , LEU A:172 , LEU A:230 , NAG A:800 , BMA A:802 , HOH A:934 , HOH A:1194 , HOH A:1254BINDING SITE FOR RESIDUE NAG A 801
10BC1SOFTWARENAG A:801 , HOH A:1254BINDING SITE FOR RESIDUE BMA A 802
11BC2SOFTWAREASN A:155 , HOH A:1260BINDING SITE FOR RESIDUE NAG A 700
12BC3SOFTWARETHR A:525 , HOH A:951 , HOH A:954 , HOH A:1019 , HOH A:1088BINDING SITE FOR RESIDUE CA A 901
13BC4SOFTWARELEU A:338 , ARG A:433 , PRO A:434 , GLU A:435 , PHE A:499 , GLU A:503 , GLU A:526 , HOH A:954 , HOH A:1095 , HOH A:1190BINDING SITE FOR RESIDUE GOL A 900

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:340 -A:385
2A:468 -A:471

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:313 -Pro A:314
2Leu A:488 -Pro A:489

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_MNS1_YEAST_001 *D40YMNS1_YEAST  ---  ---AD40Y
2UniProtVAR_MNS1_YEAST_002 *D376LMNS1_YEAST  ---  ---AD376L
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1DL2)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YJR131W1YJR131W.1X:667634-6692831650MNS1_YEAST1-5495491A:34-549 (gaps)516

(-) 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:510
 aligned with MNS1_YEAST | P32906 from UniProtKB/Swiss-Prot  Length:549

    Alignment length:516
                                    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       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543      
           MNS1_YEAST    34 GAGEMRDRIESMFLESWRDYSKHGWGYDVYGPIEHTSHNMPRGNQPLGWIIVDSVDTLMLMYNSSTLYKSEFEAEIQRSEHWINDVLDFDIDAEVNVFETTIRMLGGLLSAYHLSDVLEVGNKTVYLNKAIDLGDRLALAFLSTQTGIPYSSINLHSGQAVKNHADGGASSTAEFTTLQMEFKYLAYLTGNRTYWELVERVYEPLYKNNDLLNTYDGLVPIYTFPDTGKFGASTIRFGSRGDSFYEYLLKQYLLTHETLYYDLYRKSMEGMKKHLLAQSKPSSLWYIGEREQGLHGQLSPKMDHLVCFMGGLLASGSTEGLSIHEARRRPFFSLSLERKSDWDLAKGITDTCYQMYKQSSSGLAPEIVVFNDGNIKQDGWWRSSVGDFFVKPLDRHNLQRPETVESIMFMYHLSHDHKYREWGAEIATSFFENTCVDCNDPKLRRFTSLSDCITLPTKKSNNMESFWLAETLKYLYILFLDEFDLTKVVFNTEAHPFPVLDEEILKSQSLTTGWSL 549
               SCOP domains d1dl2a_ A: Class I alpha-1;2-mannosidase, catalytic domain                                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1dl2A00 A:34-549  [code=1.50.10.50, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh....eee....eee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.......eeehhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh........eee.....ee...hhhhheehhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee......eee.............eee.hhhhhhhhhhhhhhh..hhhhhh.....h-----hhhhhhhhhhhhhhhhhhhh........eeee......-...ee.....eeehhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhee........ee..eee......ee....hhhhhhhhhhhhhhhh........eee.....eee..hhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------Y-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:34-549 (gaps) UniProt: 1-549 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Transcript 1
                 1dl2 A  34 GAGEMRDRIESMFLESWRDYSKHGWGYDVYGPIEHTSHNMPRGNQPLGWIIVDSVDTLMLMYNSSTLYKSEFEAEIQRSEHWINDVLDFDIDAEVNVFETTIRMLGGLLSAYHLSDVLEVGNKTVYLNKAIDLGDRLALAFLSTQTGIPYSSINLHSGQAVKNHADGGASSTAEFTTLQMEFKYLAYLTGNRTYWELVERVYEPLYKNNDLLNTYDGLVPIYTFPDTGKFGASTIRFGSRGDSFYEYLLKQYLLTHETLYYDLYRKSMEGMKKHLLAQSKPSSLWYIGEREQGLHGQLSPKMDHLVCFMGGLLASGSTEGLSIHEARRRPFFS-----KSDWDLAKGITDTCYQMYKQSSSGLAPEIVVFNDGNIK-DGWWRSSVGDFFVKPLDRHNLQRPETVESIMFMYHLSHDHKYREWGAEIATSFFENTCVDCNDPKLRRFTSLSDCITLPTKKSNNMESFWLAETLKYLYILFLDEFDLTKVVFNTEAHPFPVLDEEILKSQSLTTGWSL 549
                                    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       383       393       403     | 413       423       433       443       453       463       473       483       493       503       513       523       533       543      
                                                                                                                                                                                                                                                                                                                                                                      366   372                                  409 |                                                                                                                                          
                                                                                                                                                                                                                                                                                                                                                                                                                   411
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DL2)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MNS1_YEAST | P32906)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004571    mannosyl-oligosaccharide 1,2-alpha-mannosidase activity    Catalysis of the hydrolysis of the terminal (1->2)-linked alpha-D-mannose residues in an oligo-mannose oligosaccharide.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006491    N-glycan processing    The conversion of N-linked glycan (N = nitrogen) structures from the initially transferred oligosaccharide to a mature form, by the actions of glycosidases and glycosyltransferases. The early processing steps are conserved and play roles in glycoprotein folding and trafficking.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0035977    protein deglycosylation involved in glycoprotein catabolic process    The removal of sugar residues from a glycosylated protein that contributes to the breakdown of a glycoprotein.
    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.
    GO:0030433    ubiquitin-dependent ERAD pathway    The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein ubiquitination necessary for correct substrate transfer, transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.
    GO:0097466    ubiquitin-dependent glycoprotein ERAD pathway    An ERAD pathway whereby endoplasmic reticulum (ER)-resident glycoproteins are targeted for degradation. Includes differential processing of the glycoprotein sugar chains, retrotranslocation to the cytosol and degradation by the ubiquitin-proteasome pathway. A glycoprotein is a compound in which a carbohydrate component is covalently bound to a protein component.
cellular component
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    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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  1dl2
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  3.2.1.113
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 Related Entries

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

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        MNS1_YEAST | P32906: 1g6i

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