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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CLASS I ALPHA-1,2-MANNOSIDASE IN COMPLEX WITH THIO-DISACCHARIDE SUBSTRATE ANALOGUE
 
Authors :  K. Karaveg, W. Tempel, Z. J. Liu, A. Siriwardena, K. W. Moremen, B. C. Wang
Date :  20 Aug 04  (Deposition) - 22 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.41
Chains :  Asym./Biol. Unit :  A
Keywords :  Mannosidase, Substrate Analogue, Glycosyl Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Karaveg, A. Siriwardena, W. Tempel, Z. J. Liu, J. Glushka, B. C. Wang, K. W. Moremen
Mechanism Of Class 1 (Glycosylhydrolase Family 47) {Alpha}-Mannosidases Involved In N-Glycan Processing And Endoplasmic Reticulum Quality Control.
J. Biol. Chem. V. 280 16197 2005
PubMed-ID: 15713668  |  Reference-DOI: 10.1074/JBC.M500119200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENDOPLASMIC RETICULUM MANNOSYL-OLIGOSACCHARIDE 1, 2-ALPHA-MANNOSIDASE
    ChainsA
    EC Number3.2.1.113
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System Taxid4922
    FragmentRESIDUES 243-699
    GeneMAN1B1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymER ALPHA-1,2-MANNOSIDASE, MANNOSIDASE ALPHA CLASS 1B MEMBER 1, MAN9GLCNAC2-SPECIFIC PROCESSING ALPHA- MANNOSIDASE, UNQ747/PRO1477

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1BU11Ligand/Ion1,4-BUTANEDIOL
2CA1Ligand/IonCALCIUM ION
3SMD1Ligand/IonMETHYL-2-S-(ALPHA-D-MANNOPYRANOSYL)-2-THIO-ALPHA-D-MANNOPYRANOSIDE
4SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:688 , SMD A:1003 , HOH A:1005 , HOH A:1008 , HOH A:1009 , HOH A:1010BINDING SITE FOR RESIDUE CA A 1001
2AC2SOFTWARELYS A:262 , LYS A:266 , THR A:451 , HIS A:452 , LEU A:453BINDING SITE FOR RESIDUE SO4 A 1002
3AC3SOFTWAREARG A:334 , ALA A:396 , GLU A:397 , ARG A:461 , ASP A:463 , LEU A:525 , ARG A:597 , PRO A:598 , GLU A:599 , GLU A:663 , THR A:688 , GLU A:689 , CA A:1001 , HOH A:1009 , HOH A:1010 , HOH A:1012 , HOH A:1021 , HOH A:1302BINDING SITE FOR RESIDUE SMD A 1003
4AC4SOFTWAREGLY A:302 , HIS A:429 , GLY A:430 , SER A:432 , HOH A:1057 , HOH A:1067BINDING SITE FOR RESIDUE BU1 A 1004

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:527 -A:556

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:503 -Pro A:504

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_066592R334CMA1B1_HUMANDisease (MRT15)387906886AR334C
2UniProtVAR_066593E397KMA1B1_HUMANDisease (MRT15)387906885AE397K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X9D)

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003715891aENSE00001455607chr9:139981400-139981670271MA1B1_HUMAN1-73730--
1.2ENST000003715892ENSE00001792863chr9:139982527-139982635109MA1B1_HUMAN74-110370--
1.4ENST000003715894ENSE00001280716chr9:139983321-139983457137MA1B1_HUMAN110-155460--
1.6ENST000003715896ENSE00001280706chr9:139990689-139990843155MA1B1_HUMAN156-207520--
1.7ENST000003715897ENSE00001280699chr9:139992280-139992389110MA1B1_HUMAN207-244380--
1.8ENST000003715898ENSE00001280694chr9:139994148-139994333186MA1B1_HUMAN244-306631A:245-30662
1.9ENST000003715899ENSE00001280687chr9:139995457-139995605149MA1B1_HUMAN306-355501A:306-35550
1.10aENST0000037158910aENSE00001280681chr9:139995936-139996124189MA1B1_HUMAN356-418631A:356-41863
1.11bENST0000037158911bENSE00001280672chr9:140000577-140000767191MA1B1_HUMAN419-482641A:419-48264
1.12ENST0000037158912ENSE00001280664chr9:140001141-140001261121MA1B1_HUMAN482-522411A:482-52241
1.13aENST0000037158913aENSE00001280655chr9:140001702-140001899198MA1B1_HUMAN523-588661A:523-58866
1.14aENST0000037158914aENSE00001280645chr9:140001983-140002114132MA1B1_HUMAN589-632441A:589-63244
1.14dENST0000037158914dENSE00001810926chr9:140002840-140003635796MA1B1_HUMAN633-699671A:633-697 (gaps)65

(-) 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:452
 aligned with MA1B1_HUMAN | Q9UKM7 from UniProtKB/Swiss-Prot  Length:699

    Alignment length:453
                                   254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694   
          MA1B1_HUMAN   245 HLNYRQKGVIDVFLHAWKGYRKFAWGHDELKPVSRSFSEWFGLGLTLIDALDTMWILGLRKEFEEARKWVSKKLHFEKDVDVNLFESTIRILGGLLSAYHLSGDSLFLRKAEDFGNRLMPAFRTPSKIPYSDVNIGTGVAHPPRWTSDSTVAEVTSIQLEFRELSRLTGDKKFQEAVEKVTQHIHGLSGKKDGLVPMFINTHSGLFTHLGVFTLGARADSYYEYLLKQWIQGGKQETQLLEDYVEAIEGVRTHLLRHSEPSKLTFVGELAHGRFSAKMDHLVCFLPGTLALGVYHGLPASHMELAQELMETCYQMNRQMETGLSPEIVHFNLYPQPGRRDVEVKPADRHNLLRPETVESLFYLYRVTGDRKYQDWGWEILQSFSRFTRVPSGGYSSINNVQDPQKPEPRDKMESFFLGETLKYLFLLFSDDPNLLSLDAYVFNTEAHPLPIWT 697
               SCOP domains d1x9da_ A: Class I alpha-1;2-mannosidase, catalytic domain                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1x9dA00 A:245-697  [code=1.50.10.50, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains -----------Glyco_hydro_47-1x9dA01 A:256-695                                                                                                                                                                                                                                                                                                                                                                                                                        -- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh....eee....eee.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eee.....ee......eeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...........eee.....ee...ee.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhheee......eee.eee..eee.eee...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh........eee..............hhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..........................hhhhhhhhhhhhhhhh..-.......eee.....eee... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------C--------------------------------------------------------------K------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.8  PDB: A:245-306 UniProt: 244-306 [INCOMPLETE]        -------------------------------------------------Exon 1.10a  PDB: A:356-418 UniProt: 356-418                    Exon 1.11b  PDB: A:419-482 UniProt: 419-482                     ----------------------------------------Exon 1.13a  PDB: A:523-588 UniProt: 523-588                       Exon 1.14a  PDB: A:589-632 UniProt: 589-632 Exon 1.14d  PDB: A:633-697 (gaps) UniProt: 633-699 [INCOMPLETE]   Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------Exon 1.9  PDB: A:306-355 UniProt: 306-355         ------------------------------------------------------------------------------------------------------------------------------Exon 1.12  PDB: A:482-522                ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1x9d A 245 HLNYRQKGVIDVFLHAWKGYRKFAWGHDELKPVSRSFSEWFGLGLTLIDALDTMWILGLRKEFEEARKWVSKKLHFEKDVDVNLFESTIRILGGLLSAYHLSGDSLFLRKAEDFGNRLMPAFRTPSKIPYSDVNIGTGVAHPPRWTSDSTVAEVTSIQLEFRELSRLTGDKKFQEAVEKVTQHIHGLSGKKDGLVPMFINTHSGLFTHLGVFTLGARADSYYEYLLKQWIQGGKQETQLLEDYVEAIEGVRTHLLRHSEPSKLTFVGELAHGRFSAKMDHLVCFLPGTLALGVYHGLPASHMELAQELMETCYQMNRQMETGLSPEIVHFNLYPQPGRRDVEVKPADRHNLLRPETVESLFYLYRVTGDRKYQDWGWEILQSFSRFTRVPSGGYSSINNVQDPQKPEPRDKMESFFLGETLKYLFLLFSDD-NLLSLDAYVFNTEAHPLPIWT 697
                                   254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674| |    684       694   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                        675 |                    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          677                    

   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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: 6_Hairpin (120)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MA1B1_HUMAN | Q9UKM7)
molecular function
    GO:0004559    alpha-mannosidase activity    Catalysis of the hydrolysis of terminal, non-reducing alpha-D-mannose residues in alpha-D-mannosides.
    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:1904380    endoplasmic reticulum mannose trimming    Any protein alpha-1,2-demannosylation that takes place in the endoplasmic reticulum quality control compartment (ERQC).
    GO:1904382    mannose trimming involved in glycoprotein ERAD pathway    The removal of one or more alpha 1,2-linked mannose residues from a mannosylated protein that occurs as part of glycoprotein ER-associated glycoprotein degradation (gpERAD).
    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:0009311    oligosaccharide metabolic process    The chemical reactions and pathways involving oligosaccharides, molecules with between two and (about) 20 monosaccharide residues connected by glycosidic linkages.
    GO:0036508    protein alpha-1,2-demannosylation    The removal of one or more alpha 1,2-linked mannose residues from a mannosylated 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:0036509    trimming of terminal mannose on B branch    The removal of an alpha-1,2-linked mannose from the B-chain of a glycoprotein oligosaccharide in the endoplasmic reticulum.
    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.
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: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:0044322    endoplasmic reticulum quality control compartment    A subcompartment of the endoplasmic reticulum in which proteins with improper or incorrect folding accumulate. Enzymes in this compartment direct proteins with major folding problems to translocation to the cytosol and degradation, and proteins with minor folding problems to the ER, to interact with chaperon proteins.
    GO:1903561    extracellular vesicle    Any vesicle that is part of the extracellular region.
    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
        MA1B1_HUMAN | Q9UKM71fmi 1fo2 1fo3 5kij 5kk7

(-) Related Entries Specified in the PDB File

1fmi MOLECULAR REPLACEMENT MODEL OF HUMAN CLASS I 1,2-MANNOSIDASE