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(-) Description

Title :  GOLGI ALPHA-MANNOSIDASE II IN COMPLEX WITH A DIASTEREOMER OF SELENO-SALACINOL
 
Authors :  D. A. Kuntz, A. Ghavami, B. D. Johnston, B. M. Pinto, D. R. Rose
Date :  18 Jun 04  (Deposition) - 01 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. A. Kuntz, A. Ghavami, B. D. Johnston, B. M. Pinto, D. R. Rose
Insights Into The Mechanism Of Drosophila Melanogaster Golg A-Mannosidase Ii Through Crystallographic Analysis Of The Interactions With Analogues Of The Naturally Occurring Glycomimetic Salacinol
Tetrahedron Asymmetry V. 16 25 2005
PubMed: search

(-) Compounds

Molecule 1 - ALPHA-MANNOSIDASE II
    ChainsA
    EC Number3.2.1.114
    EngineeredYES
    Expression SystemDROSOPHILA MELANOGASTER
    Expression System Cell LineS2 CELLS
    Expression System CommonFRUIT FLY
    Expression System Taxid7227
    FragmentFAMILY 38 CATALYTIC DOMAIN
    GeneALPHA-MAN-II, GMII, CG18474/CG18802/CG8139
    MutationYES
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
    SynonymMANNOSYL-OLIGOSACCHARIDE 1,3-1,6-ALPHA-MANNOSIDASE, MAN II, GOLGI ALPHA-MANNOSIDASE II, AMAN II

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1BLT1Ligand/Ion1,4-DIDEOXY-1,4-[[2R,3R)-2,4-DIHYDROXY-3-(SULFOXY)BUTYL]EPISELENONIUMYLIDENE]-D-ARABINITOL INNER SALT
2MRD2Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
4ZN1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:194BINDING SITE FOR RESIDUE NAG A 1046
2AC2SOFTWAREHIS A:90 , ASP A:92 , ASP A:204 , HIS A:471 , BLT A:1300BINDING SITE FOR RESIDUE ZN A 1400
3AC3SOFTWAREASP A:92 , TRP A:95 , ASP A:204 , PHE A:206 , ARG A:228 , TYR A:269 , ASP A:340 , ASP A:341 , HIS A:471 , ASP A:472 , TYR A:727 , ARG A:876 , GLY A:877 , ZN A:1400 , HOH A:1598 , HOH A:1599 , HOH A:1785 , HOH A:1787 , HOH A:2246BINDING SITE FOR RESIDUE BLT A 1300
4AC4SOFTWARELYS A:63 , GLN A:64 , HIS A:273 , HOH A:1577 , HOH A:1632 , HOH A:1634 , HOH A:1635BINDING SITE FOR RESIDUE MRD A 1100
5AC5SOFTWAREASP A:106 , ASP A:341 , PHE A:342BINDING SITE FOR RESIDUE MRD A 1200

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:31 -A:1032
2A:275 -A:282
3A:283 -A:297
4A:902 -A:987
5A:1000 -A:1009

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:405 -Thr A:406
2Trp A:531 -Pro A:532

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TQW)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1TQW)

(-) 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:1014
 aligned with MAN2_DROME | Q24451 from UniProtKB/Swiss-Prot  Length:1108

    Alignment length:1014
                                   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       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923       933       943       953       963       973       983       993      1003      1013      1023      1033      1043      1053      1063      1073      1083      1093      1103    
          MAN2_DROME     94 CQDVVQDVPNVDVQMLELYDRMSFKDIDGGVWKQGWNIKYDPLKYNAHHKLKVFVVPHSHNDPGWIQTFEEYYQHDTKHILSNALRHLHDNPEMKFIWAEISYFARFYHDLGENKKLQMKSIVKNGQLEFVTGGWVMPDEANSHWRNVLLQLTEGQTWLKQFMNVTPTASWAIDPFGHSPTMPYILQKSGFKNMLIQRTHYSVKKELAQQRQLEFLWRQIWDNKGDTALFTHMMPFYSYDIPHTCGPDPKVCCQFDFKRMGSFGLSCPWKVPPRTISDQNVAARSDLLVDQWKKKAELYRTNVLLIPLGDDFRFKQNTEWDVQRVNYERLFEHINSQAHFNVQAQFGTLQEYFDAVHQAERAGQAEFPTLSGDFFTYADRSDNYWSGYYTSRPYHKRMDRVLMHYVRAAEMLSAWHSWDGMARIEERLEQARRELSLFQHHDGITGTAKTHVVVDYEQRMQEALKACQMVMQQSVYRLLTKPSIYSPDFSFSYFTLDDSRWPGSGVEDSRTTIILGEDILPSKHVVMHNTLPHWREQLVDFYVSSPFVSVTDLANNPVEAQVSPVWSWHHDTLTKTIHPQGSTTKYRIIFKARVPPMGLATYVLTISDSKPEHTSYASNLLLRKNPTSLPLGQYPEDVKFGDPREISLRVGNGPTLAFSEQGLLKSIQLTQDSPHVPVHFKFLKYGVRSHGDRSGAYLFLPNGPASPVELGQPVVLVTKGKLESSVSVGLPSVVHQTIMRGGAPEIRNLVDIGSLDNTEIVMRLETHIDSGDIFYTDLNGLQFIKRRRLDKLPLQANYYPIPSGMFIEDANTRLTLLTGQPLGGSSLASGELEIMQDRRLASDDERGLGQGVLDNKPVLHIYRLVLEKVNNCVRPSELHPAGYLTSAAHKASQSLLDPLDKFIFAENEWIGAQGQFGGDHPSAREDLDVSVMRRLTKSSAKTQRVGYVLHRTNLMQCGTPEEHTQKLDVCHLLPNVARCERTTLTFLQNLEHLDGMVAPEVCPMETAAYVSSHS 1107
               SCOP domains d1tqwa3 A:31-411 Golgi alpha-mannosidase II                                                                                                                                                                                                                                                                                                                                                  d1tqwa1 A:412-522 Golgi alpha-mannosidase II                                                                   d1tqwa2 A:523-1044 Golgi alpha-mannosidase II                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1tqwA01 A:31-411 Glycoside hydrolase 38, N terminal domain                                                                                                                                                                                                                                                                                                                                   1tqwA02 A:412-522 Families 57/38 glycoside transferase; middle domain                                          1tqwA03 A:523-647,A:928-949 Golgi alpha-mannosidase II                                                                       1tqwA04 A:648-927 Golgi alpha-mannosidase II; domain 4                                                                                                                                                                                                                                  1tqwA03               1tqwA05 A:950-1044  [code=2.60.40.1360, no name defined]                                        CATH domains
               Pfam domains ---------------------------------------------------Glyco_hydro_38-1tqwA01 A:82-408                                                                                                                                                                                                                                                                                                        ----Alpha-mann_mid-1tqwA03 A:413-490                                              --------------------------------------------------------------Glyco_hydro_38C-1tqwA02 A:553-1040                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---- Pfam domains
         Sec.struct. author ............eehhhhhhhh..................hhhhh.....eeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhhh..eee.............hhhhhhhhhhhhhhhhhhhhh....eeee.......hhhhhhhhh....eeee...hhhhhhhhhhh...eeee...........eeeee......hhhhh...hhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhh.....eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhh......eee......eee..ee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............eeee..............ee........eeeeeeee.....eeeeeeeee....eeeee....ee.eeeeeeeeeeee....eeeeeeeeeeeeeeeeeee...eeeeeeeee.......eee.eeeee................eee....eeee.....eeee.....eeeee.......eeeeeeeeee....................ee.......eeeee....eeeeeee..eeeeeee.....eeeeee.......eeeeeeeee......eeeeee...eeeeee.....hhhhhheee..eeeee...eeeeeee...eeee.....eeeeeeeee..................eeeeeeeeeee............ee..hhhhhhhhhhhhh..eeeee..........ee..........eeeeeeee........eeeeeeeee................hhhhh...eeeeeee......eeee.hhhh........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1tqw A   31 CQDVVQDVPNVDVQMLELYDRMSFKDIDGGVWKQGWNIKYDPLKYNAHHKLKVFVVPHSHNDPGWIQTFEEYYQHDTKHILSNALRHLHDNPEMKFIWAEISYFARFYHDLGENKKLQMKSIVKNGQLEFVTGGWVMPDEANSHWRNVLLQLTEGQTWLKQFMNVTPTASWAIDPFGHSPTMPYILQKSGFKNMLIQRTHYSVKKELAQQRQLEFLWRQIWDNKGDTALFTHMMPFYSYDIPHTCGPDPKVCCQFDFKRMGSFGLSCPWKVPPRTISDQNVAARSDLLVDQWKKKAELYRTNVLLIPLGDDFRFKQNTEWDVQRVNYERLFEHINSQAHFNVQAQFGTLQEYFDAVHQAERAGQAEFPTLSGDFFTYADRSDNYWSGYYTSRPYHKRMDRVLMHYVRAAEMLSAWHSWDGMARIEERLEQARRELSLFQHHDGITGTAKTHVVVDYEQRMQEALKACQMVMQQSVYRLLTKPSIYSPDFSFSYFTLDDSRWPGSGVEDSRTTIILGEDILPSKHVVMHNTLPHWREQLVDFYVSSPFVSVTDLANNPVEAQVSPVWSWHHDTLTKTIHPQGSTTKYRIIFKARVPPMGLATYVLTISDSKPEHTSYASNLLLRKNPTSLPLGQYPEDVKFGDPREISLRVGNGPTLAFSEQGLLKSIQLTQDSPHVPVHFKFLKYGVRSHGDRSGAYLFLPNGPASPVELGQPVVLVTKGKLESSVSVGLPSVVHQTIMRGGAPEIRNLVDIGSLDNTEIVMRLETHIDSGDIFYTDLNGLQFIKRRRLDKLPLQANYYPIPSGMFIEDANTRLTLLTGQPLGGSSLASGELEIMQDRRLASDDERGLGQGVLDNKPVLHIYRLVLEKVNNCVRPSKLHPAGYLTSAAHKASQSLLDPLDKFIFAENEWIGAQGQFGGDHPSAREDLDVSVMRRLTKSSAKTQRVGYVLHRTNLMQCGTPEEHTQKLDVCHLLPNVARCERTTLTFLQNLEHLDGMVAPEVCPMETAAYVSSHS 1044
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      1040    

   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  (3, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (5, 5)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: GH_CE (28)

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MAN2_DROME | Q24451)
molecular function
    GO:0004559    alpha-mannosidase activity    Catalysis of the hydrolysis of terminal, non-reducing alpha-D-mannose residues in alpha-D-mannosides.
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0015923    mannosidase activity    Catalysis of the hydrolysis of mannosyl compounds, substances containing a group derived from a cyclic form of mannose or a mannose derivative.
    GO:0004572    mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity    Catalysis of the hydrolysis of the terminal (1->3)- and (1->6)-linked alpha-D-mannose residues in the mannosyl-oligosaccharide Man(5)(GlcNAc)(3).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0035010    encapsulation of foreign target    Events resulting in the formation of a multilayered cellular sheath surrounding an invader and thus preventing its development. This defense mechanism is often seen in insects in response to nematodes or parasitoids, which are too large to be phagocytosed by individual hemocytes. In some organisms the capsule is blackened due to melanization.
    GO:0006013    mannose metabolic process    The chemical reactions and pathways involving mannose, the aldohexose manno-hexose, the C-2 epimer of glucose. The D-(+)-form is widely distributed in mannans and hemicelluloses and is of major importance in the core oligosaccharide of N-linked oligosaccharides of glycoproteins.
    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:0006487    protein N-linked glycosylation    A protein glycosylation process in which a carbohydrate or carbohydrate derivative unit is added to a protein via the N4 atom of peptidyl-asparagine, the omega-N of arginine, or the N1' atom peptidyl-tryptophan.
    GO:0006517    protein deglycosylation    The removal of sugar residues from a glycosylated protein.
    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:0016063    rhodopsin biosynthetic process    The chemical reactions and pathways resulting in the formation of rhodopsin, a brilliant purplish-red, light-sensitive visual pigment found in the rod cells of the retinas.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0005795    Golgi stack    The set of thin, flattened membrane-bounded compartments, called cisternae, that form the central portion of the Golgi complex. The stack usually comprises cis, medial, and trans cisternae; the cis- and trans-Golgi networks are not considered part of the stack.
    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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        MAN2_DROME | Q244511hty 1hww 1hxk 1ps3 1qwn 1qwu 1qx1 1r33 1r34 1tqs 1tqt 1tqu 1tqv 2alw 2f18 2f1a 2f1b 2f7o 2f7p 2f7q 2f7r 2fyv 2ow6 2ow7 3blb 3bub 3bud 3bui 3bup 3buq 3bvt 3bvu 3bvv 3bvw 3bvx 3cv5 3czn 3czs 3d4y 3d4z 3d50 3d51 3d52 3ddf 3ddg 3dx0 3dx1 3dx2 3dx3 3dx4 3ejp 3ejq 3ejr 3ejs 3ejt 3eju

(-) Related Entries Specified in the PDB File

1hty 1hww 1hxk 1ps3 1qwn 1qwu 1qx1 1r33 1r34 1tqs 1tqt 1tqu 1tqv