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(-) Description

Title :  STRUCTURE OF THE N-TERMINAL DOMAIN OF PEX1 AAA-ATPASE: CHARACTERIZATION OF A PUTATIVE ADAPTOR-BINDING DOMAIN
 
Authors :  K. Shiozawa, N. Maita, K. Tomii, A. Seto, N. Goda, H. Tochio, Y. Akiyama, T. Shimizu, M. Shirakawa, H. Hiroaki
Date :  25 Jun 04  (Deposition) - 07 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A
Keywords :  N-Terminal Domain, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Shiozawa, N. Maita, K. Tomii, A. Seto, N. Goda, Y. Akiyama, T. Shimizu, M. Shirakawa, H. Hiroaki
Structure Of The N-Terminal Domain Of Pex1 Aaa-Atpase: Characterization Of A Putative Adaptor-Binding Domain
J. Biol. Chem. V. 279 50060 2004
PubMed-ID: 15328346  |  Reference-DOI: 10.1074/JBC.M407837200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEROXISOME BIOGENESIS FACTOR 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: PEX1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:30 , GLY A:63 , ARG A:64 , HIS A:65 , HOH A:197BINDING SITE FOR RESIDUE SO4 A 182

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WLF)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Met A:161 -Pro A:162

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WLF)

(-) 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:164
 aligned with PEX1_MOUSE | Q5BL07 from UniProtKB/Swiss-Prot  Length:1284

    Alignment length:167
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       
           PEX1_MOUSE    13 GGAVVTVAFTNARDCFLHLPRRLVAQLHLLQNQAIEVASDHQPTYLSWVEGRHFNDQSENVAEINRQVGQKLGLSSGDQVFLRPCSHVVSCQQVEVEPLSADDWEILELHAISLEQHLLDQIRIVFPKAVVPIWVDQQTYIFIQIVTLMPAAPYGRLETNTKLLIQP 179
               SCOP domains d1wlfa2 A:13-99 Peroxisome biogenesis factor 1 (PEX-1),    N-terminal domain           d1wlfa1 A:100-179 Peroxisome biogenesis factor 1 (PEX-1), domain 2               SCOP domains
               CATH domains 1wlfA01 A:13-99  [code=2.40.40.20, no name defined]                                    1wlfA02 A:100-179  [code=3.10.330.10, no name defined]                           CATH domains
               Pfam domains -PEX-2N-1wlfA02 A:14-99                                                                ---PEX-1N-1wlfA01 A:103-179                                                      Pfam domains
         Sec.struct. author ..eeeeeeee......eeehhhhhhhh.......eeee.....eee.eee.....---..eeeeehhhhhhh......eeeeee....ee..eeeeee.hhhhhhhhhhh..hhhhhhhhhh.ee....eeeee.....eeeeeeeeee.....ee.....eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wlf A  13 GGAVVTVAFTNARDCFLHLPRRLVAQLHLLQNQAIEVASDHQPTYLSWVEGRHFN---ENVAEINRQVGQKLGLSSGDQVFLRPCSHVVSCQQVEVEPLSADDWEILELHAISLEQHLLDQIRIVFPKAVVPIWVDQQTYIFIQIVTLMPAAPYGRLETNTKLLIQP 179
                                    22        32        42        52        62    |   72        82        92       102       112       122       132       142       152       162       172       
                                                                                 67  71
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Cdc48_2-like (11)
(-)
Clan: no clan defined [family: PEX-2N] (1)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PEX1_MOUSE | Q5BL07)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0042623    ATPase activity, coupled    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction directly drives some other reaction, for example ion transport across a membrane.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    GO:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0060152    microtubule-based peroxisome localization    The microtubule-based process in which a peroxisome is transported to, and/or maintained in, a specific location. A peroxisome is a small membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules.
    GO:0007031    peroxisome organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a peroxisome. A peroxisome is a small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules.
    GO:0016558    protein import into peroxisome matrix    The import of proteins into the peroxisomal matrix. A peroxisome targeting signal (PTS) binds to a soluble receptor protein in the cytosol, and the resulting complex then binds to a receptor protein in the peroxisome membrane and is imported. The cargo protein is then released into the peroxisome matrix.
    GO:0006625    protein targeting to peroxisome    The process of directing proteins towards the peroxisome, usually using signals contained within the protein.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005778    peroxisomal membrane    The lipid bilayer surrounding a peroxisome.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

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