1NXC - JenaLib

Title :   STRUCTURE OF MOUSE GOLGI ALPHA-1,2-MANNOSIDASE IA REVEALS THE MOLECULAR BASIS FOR SUBSTRATE SPECIFICITY AMONG CLASS I ENZYMES (FAMILY 47 GLYCOSIDASES)

Authors :   W. Tempel, Z. -J. Liu, K. Karaveg, J. Rose, K. W. Moremen, B. -C. Wang, Sou Collaboratory For Structural Genomics (Secsg)

Date :   10 Feb 03 (Deposition) - 04 May 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.51

Chains :   Asym./Biol. Unit : A

Keywords :   Mannosidase, Glycosidase, Structural Genomics, Psi, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Secsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Tempel, K. Karaveg, Z. -J. Liu, J. Rose, B. -C. Wang, K. W. Moremen
Structure Of Mouse Golgi Alpha-Mannosidase Ia Reveals The Molecular Basis For Substrate Specificity Among Class 1 (Family 47 Glycosylhydrolase) Alpha1, 2-Mannosidases
J. Biol. Chem. V. 279 29774 2004
PubMed-ID: 15102839 | Reference-DOI: 10.1074/JBC.M403065200

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (9, 9)

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	NAG A:2 , TRP A:341 , GLU A:512 , ASN A:515 , HOH A:1060 , HOH A:1104 , HOH A:1227 , HOH A:1248 , HOH A:1294	BINDING SITE FOR RESIDUE NAG A 1
2	AC2	SOFTWARE	NAG A:1 , BMA A:3 , MAN A:7 , TRP A:341 , LEU A:413 , HOH A:1045 , HOH A:1243 , HOH A:1322	BINDING SITE FOR RESIDUE NAG A 2
3	AC3	SOFTWARE	NAG A:2 , MAN A:4 , MAN A:5 , HOH A:1117 , HOH A:1184	BINDING SITE FOR RESIDUE BMA A 3
4	AC4	SOFTWARE	BMA A:3 , MAN A:6 , MAN A:7 , LEU A:413 , GLU A:524 , HOH A:1045 , HOH A:1172 , HOH A:1262	BINDING SITE FOR RESIDUE MAN A 4
5	AC5	SOFTWARE	MAN A:4 , PHE A:281 , ALA A:350 , GLU A:351 , LEU A:413 , ASP A:415 , HOH A:1012 , HOH A:1036 , HOH A:1058 , HOH A:1079	BINDING SITE FOR RESIDUE MAN A 6
6	AC6	SOFTWARE	NAG A:2 , MAN A:4 , HOH A:1126 , HOH A:1197 , HOH A:1243	BINDING SITE FOR RESIDUE MAN A 7
7	AC7	SOFTWARE	BMA A:3 , MAN A:8 , SER A:233 , HOH A:1270	BINDING SITE FOR RESIDUE MAN A 5
8	AC8	SOFTWARE	MAN A:5 , SER A:455 , GLY A:456 , HOH A:1139 , HOH A:1270	BINDING SITE FOR RESIDUE MAN A 8
9	AC9	SOFTWARE	THR A:635 , HOH A:1086 , HOH A:1087 , HOH A:1088 , HOH A:1089 , HOH A:1090 , HOH A:1091	BINDING SITE FOR RESIDUE CA A 656

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:467
 aligned with MA1A1_MOUSE | P45700 from UniProtKB/Swiss-Prot  Length:655

    Alignment length:467
                                   187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       
          MA1A1_MOUSE   178 FLPPVGVENREPADATIREKRAKIKEMMTHAWNNYKRYAWGLNELKPISKEGHSSSLFGNIKGATIVDALDTLFIMGMKTEFQEAKSWIKKYLDFNVNAEVSVFEVNIRFVGGLLSAYYLSGEEIFRKKAVELGVKLLPAFHTPSGIPWALLNMKSGIGRNWPWASGGSSILAEFGTLHLEFMHLSHLSGDPVFAEKVMKIRTVLNKLDKPEGLYPNYLNPSSGQWGQHHVSVGGLGDSFYEYLLKAWLMSDKTDLEAKKMYFDAVQAIETHLIRKSSGGLTYIAEWKGGLLEHKMGHLTCFAGGMFALGADGAPEARAQHYLELGAEIARTCHESYNRTYVKLGPEAFRFDGGVEAIATRQNEKYYILRPEVIETYMYMWRLTHDPKYRTWAWEAVEALESHCRVNGGYSGLRDVYIARESYDDVQQSFFLAETLKYLYLIFSDDDLLPLEHWIFNTEAHPFPILR 644
               SCOP domains d1nxca_ A: Class I alpha-1;2-mannosidase, catalytic domain                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1nxcA00 A:178-644  [code=1.50.10.50, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------Glyco_hydro_47-1nxcA01 A:204-642                                                                                                                                                                                                                                                                                                                                                                                                                       -- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....eee.hhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eee.....ee....hhhhheehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhh...ee..........ee.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhheee.....eee.eee..eee.eee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh........eee..........hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..ee.................hhhhhhhhhhhhhhhh..........eee.....eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nxc A 178 FLPPVGVENREPADATIREKRAKIKEMMTHAWNNYKRYAWGLNELKPISKEGHSSSLFGNIKGATIVDALDTLFIMGMKTEFQEAKSWIKKYLDFNVNAEVSVFEVNIRFVGGLLSAYYLSGEEIFRKKAVELGVKLLPAFHTPSGIPWALLNMKSGIGRNWPWASGGSSILAEFGTLHLEFMHLSHLSGDPVFAEKVMKIRTVLNKLDKPEGLYPNYLNPSSGQWGQHHVSVGGLGDSFYEYLLKAWLMSDKTDLEAKKMYFDAVQAIETHLIRKSSGGLTYIAEWKGGLLEHKMGHLTCFAGGMFALGADGAPEARAQHYLELGAEIARTCHESYNRTYVKLGPEAFRFDGGVEAIATRQNEKYYILRPEVIETYMYMWRLTHDPKYRTWAWEAVEALESHCRVNGGYSGLRDVYIARESYDDVQQSFFLAETLKYLYLIFSDDDLLPLEHWIFNTEAHPFPILR 644
                                   187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637

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)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (MA1A1_MOUSE | P45700)

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: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: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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0005793	endoplasmic reticulum-Golgi intermediate compartment	A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi and Golgi-to-ER transport.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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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