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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CLASS I ALPHA1,2-MANNOSIDASE
 
Authors :  F. Vallee, K. Karaveg, A. Herscovics, K. W. Moremen, P. L. Howell
Date :  17 Aug 00  (Deposition) - 17 Jan 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Alpha7 Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Vallee, K. Karaveg, A. Herscovics, K. W. Moremen, P. L. Howell
Structural Basis For Catalysis And Inhibition Of N-Glycan Processing Class I Alpha 1, 2-Mannosidases.
J. Biol. Chem. V. 275 41287 2000
PubMed-ID: 10995765  |  Reference-DOI: 10.1074/JBC.M006927200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENDOPLASMIC RETICULUM ALPHA-MANNOSIDASE I
    ChainsA
    EC Number3.2.1.113
    EngineeredYES
    Expression SystemSACCHAROMYCES CEREVISIAE
    Expression System CommonBAKER'S YEAST
    Expression System PlasmidPPROTA-ERMANI
    Expression System Taxid4932
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCLASS I ALPHA1,2-MANNOSIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2SO43Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:688 , HOH A:699W , HOH A:700W , HOH A:701W , HOH A:702W , HOH A:703W , HOH A:704WBINDING SITE FOR RESIDUE CA A 1C
2AC2SOFTWAREARG A:500 , HIS A:501 , HOH A:946WBINDING SITE FOR RESIDUE SO4 A 698S
3AC3SOFTWARETRP A:299 , ARG A:304 , LYS A:435 , HIS A:497 , HOH A:904WBINDING SITE FOR RESIDUE SO4 A 2S
4AC4SOFTWARETRP A:269 , TRP A:313 , LYS A:317 , HOH A:1061WBINDING SITE FOR RESIDUE SO4 A 3S

(-) 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 1FMI)

(-) Exons   (9, 9)

Asymmetric/Biological Unit (9, 9)
 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_HUMAN207-244381A:239-244 (gaps)6
1.8ENST000003715898ENSE00001280694chr9:139994148-139994333186MA1B1_HUMAN244-306631A:244-30663
1.9ENST000003715899ENSE00001280687chr9:139995457-139995605149MA1B1_HUMAN306-355501A:306-35550
1.10aENST0000037158910aENSE00001280681chr9:139995936-139996124189MA1B1_HUMAN356-418631A:356-418 (gaps)63
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:633-69765

(-) 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:456
 aligned with MA1B1_HUMAN | Q9UKM7 from UniProtKB/Swiss-Prot  Length:699

    Alignment length:459
                                   248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688         
          MA1B1_HUMAN   239 TQGTPVHLNYRQKGVIDVFLHAWKGYRKFAWGHDELKPVSRSFSEWFGLGLTLIDALDTMWILGLRKEFEEARKWVSKKLHFEKDVDVNLFESTIRILGGLLSAYHLSGDSLFLRKAEDFGNRLMPAFRTPSKIPYSDVNIGTGVAHPPRWTSDSTVAEVTSIQLEFRELSRLTGDKKFQEAVEKVTQHIHGLSGKKDGLVPMFINTHSGLFTHLGVFTLGARADSYYEYLLKQWIQGGKQETQLLEDYVEAIEGVRTHLLRHSEPSKLTFVGELAHGRFSAKMDHLVCFLPGTLALGVYHGLPASHMELAQELMETCYQMNRQMETGLSPEIVHFNLYPQPGRRDVEVKPADRHNLLRPETVESLFYLYRVTGDRKYQDWGWEILQSFSRFTRVPSGGYSSINNVQDPQKPEPRDKMESFFLGETLKYLFLLFSDDPNLLSLDAYVFNTEAHPLPIWT 697
               SCOP domains d1f mia_ A: Class I alpha-1;2-mannosidase, catalytic domain                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1fm iA00 A:239-697  [code=1.50.10.50, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...-....hhhhhhhhhhhhhhhhhhhhhh....eee....eee.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eee.....ee...--..eehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..........ee......ee...ee.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhheee......eee.eee..eee.eee...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh........eeee..........ee.hhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.........................hhhhhhhhhhhhhhhh...........eee.....eee... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------C--------------------------------------------------------------K------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.7   -------------------------------------------------------------Exon 1.9  PDB: A:306-355 UniProt: 306-355         Exon 1.10a  PDB: A:356-418 (gaps) 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 UniProt: 633-699 [INCOMPLETE]          Transcript 1 (1)
           Transcript 1 (2) -----Exon 1.8  PDB: A:244-306 UniProt: 244-306                      -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.12  PDB: A:482-522                ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1fmi A 239 AQG-PVHLNYRQKGVIDVFLHAWKGYRKFAWGHDELKPVSRSFSEWFGLGLTLIDALDTMWILGLRKEFEEARKWVSKKLHFEKDVDVNLFESTIRILGGLLSAYHLSGDSLFLRKAEDFGNRLMPAFRTPSKIPYSDVNIGTGVAHPPR--SDSTVAEVTSIQLEFRELSRLTGDKKFQEAVEKVTQHIHGLSGKKDGLVPMFINTHSGLFTHLGVFTLGARADSYYEYLLKQWIQGGKQETQLLEDYVEAIEGVRTHLLRHSEPSKLTFVGELAHGRFSAKMDHLVCFLPGTLALGVYHGLPASHMELAQELMETCYQMNRQMETGLSPEIVHFNLYPQPGRRDVEVKPADRHNLLRPETVESLFYLYRVTGDRKYQDWGWEILQSFSRFTRVPSGGYSSINNVQDPQKPEPRDKMESFFLGETLKYLFLLFSDDPNLLSLDAYVFNTEAHPLPIWT 697
                              | |  248       258       268       278       288       298       308       318       328       338       348       358       368       378       388  |    398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688         
                              | |                                                                                                                                              388  |                                                                                                                                                                                                                                                                                                                  
                            241 |                                                                                                                                                 391                                                                                                                                                                                                                                                                                                                  
                              243                                                                                                                                                                                                                                                                                                                                                                                                                                                                      

   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  (0, 0)

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

(-) 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

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        MA1B1_HUMAN | Q9UKM71fo2 1fo3 1x9d 5kij 5kk7

(-) Related Entries Specified in the PDB File

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