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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE APOLIPOPROTEIN M
 
Authors :  M. Sevvana, K. Kassler, A. Josefin, S. Weiler, B. Dahlback, H. Sticht, Y. A. Muller
Date :  09 Jul 10  (Deposition) - 13 Oct 10  (Release) - 11 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Lipid Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Sevvana, K. Kassler, J. Ahnstrom, S. Weiler, B. Dahlback, H. Sticht, Y. A. Muller
Mouse Apom Displays An Unprecedented Seven- Stranded Lipocalin Fold: Folding Decoy Or Alternative Native Fold?
J. Mol. Biol. V. 404 363 2010
PubMed-ID: 20932978  |  Reference-DOI: 10.1016/J.JMB.2010.09.062

(-) Compounds

Molecule 1 - APOLIPOPROTEIN M
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET30XA/LIC
    Expression System StrainBL21
    Expression System Taxid511693
    FragmentRESIDUES 20-190
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymAPOM, APO-M

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3NA1Ligand/IonSODIUM ION
4POL1Ligand/IonN-PROPANOL
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GOL2Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4POL2Ligand/IonN-PROPANOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:40 , GLU A:41 , TYR A:102 , GLU A:138 , ARG A:145 , POL A:1191 , HOH A:2093BINDING SITE FOR RESIDUE GOL A1190
2AC2SOFTWAREPHE A:63 , LEU A:84 , TRP A:100 , TYR A:102 , TYR A:149 , GOL A:1190BINDING SITE FOR RESIDUE POL A1191
3AC3SOFTWAREGLN A:164 , THR A:167 , SER A:168 , PHE A:172 , LYS A:173 , PHE A:175BINDING SITE FOR RESIDUE EDO A1192
4AC4SOFTWARECYS A:169BINDING SITE FOR RESIDUE NA A1193

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:95 -A:185
2A:130 -A:159

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr A:39 -Pro A:40

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XKL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XKL)

(-) Exons   (0, 0)

(no "Exon" information available for 2XKL)

(-) Sequences/Alignments

Asymmetric 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:149
 aligned with APOM_MOUSE | Q9Z1R3 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:166
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183      
           APOM_MOUSE    24 PEHSQLTALGMDDTETPEPHLGLWYFIAGAASTTEELATFDPVDNIVFNMAAGSAPRQLQLRATIRTKSGVCVPRKWTYRLTEGKGNMELRTEGRPDMKTDLFSSSCPGGIMLKETGQGYQRFLLYNRSPHPPEKCVEEFQSLTSCLDFKAFLVTPRNQEACPLSS 189
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ApoM-2xklA01 A:24-189                                                                                                                                                  Pfam domains
         Sec.struct. author ....eeeeeee............eeeeeeee.hhhhhhhhh.eeeeeeeeee.....eeeeeeeeee....eeeeeeeeee..-----------------hhhhhhh..eeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhh...eeee............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xkl A  24 PEHSQLTALGMDDTETPEPHLGLWYFIAGAASTTEELATFDPVDNIVFNMAAGSAPRQLQLRATIRTKSGVCVPRKWTYRLTE-----------------DLFSSSCPGGIMLKETGQGYQRFLLYNRSPHPPEKCVEEFQSLTSCLDFKAFLVTPRNQEACPLSS 189
                                    33        43        53        63        73        83        93       103  |      -         -|      133       143       153       163       173       183      
                                                                                                            106               124                                                                 

   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  (0, 0)

(no "SCOP Domain" information available for 2XKL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XKL)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Calycin (163)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A   (APOM_MOUSE | Q9Z1R3)
molecular function
    GO:0016209    antioxidant activity    Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
    GO:0005319    lipid transporter activity    Enables the directed movement of lipids into, out of or within a cell, or between cells.
    GO:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
biological process
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0033344    cholesterol efflux    The directed movement of cholesterol, cholest-5-en-3-beta-ol, out of a cell or organelle.
    GO:0034380    high-density lipoprotein particle assembly    The non-covalent aggregation and arrangement of proteins and lipids to form a high-density lipoprotein particle.
    GO:0034384    high-density lipoprotein particle clearance    The process in which a high-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.
    GO:0034375    high-density lipoprotein particle remodeling    The acquisition, loss or modification of a protein or lipid within a high-density lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase, with the subsequent loss of free fatty acid, and the transfer of cholesterol esters from LDL to a triglyceride-rich lipoprotein particle by cholesteryl ester transfer protein (CETP), with the simultaneous transfer of triglyceride to LDL.
    GO:0006869    lipid transport    The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0042157    lipoprotein metabolic process    The chemical reactions and pathways involving any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids.
    GO:0034445    negative regulation of plasma lipoprotein oxidation    Any process that stops, prevents, or reduces the frequency, rate or extent of lipoprotein particle oxidation, occurring in the blood plasma.
    GO:0009749    response to glucose    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.
    GO:0043691    reverse cholesterol transport    The directed movement of peripheral cell cholesterol, cholest-5-en-3-beta-ol, towards the liver for catabolism.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0034365    discoidal high-density lipoprotein particle    A newly formed high-density lipoprotein particle; consists of a phospholipid bilayer surrounded by two or more APOA1 molecules. The discoidal HDL particle is formed when lipid-free or lipid-poor APOA1 acquires phospholipids and unesterified cholesterol from either cell membranes or triglyceride-rich lipoproteins (undergoing lipolysis by lipoprotein lipase).
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0034364    high-density lipoprotein particle    A lipoprotein particle with a high density (typically 1.063-1.21 g/ml) and a diameter of 5-10 nm that contains APOAs and may contain APOCs and APOE; found in blood and carries lipids from body tissues to the liver as part of the reverse cholesterol transport process.
    GO:0034362    low-density lipoprotein particle    A lipoprotein particle, rich in cholesterol esters and low in triglycerides that is typically composed of APOB100 and APOE and has a density of 1.02-1.06 g/ml and a diameter of between 20-25 nm. LDL particles are formed from VLDL particles (via IDL) by the loss of triglyceride and gain of cholesterol ester. They transport endogenous cholesterol (and to some extent triglycerides) from peripheral tissues back to the liver.
    GO:0034366    spherical high-density lipoprotein particle    A mature high-density lipoprotein (HDL) particle, converted from discoidal HDL particles following the esterification of cholesterol in the particle by phosphatidylcholine-sterol O-acyltransferase (lecithin cholesterol acyltransferase; LCAT).
    GO:0034361    very-low-density lipoprotein particle    A triglyceride-rich lipoprotein particle that is typically composed of APOB100, APOE and APOCs and has a density of about 1.006 g/ml and a diameter of between 20-80 nm. It is found in blood and transports endogenous products (newly synthesized cholesterol and triglycerides) from the liver.

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