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(-) Description

Title :  ADP-RIBOSYLATION FACTOR-LIKE 1 (ARL1) FROM SACCHAROMYCES CEREVISIAE
 
Authors :  J. C. Amor, J. R. Horton, X. Zhu, Y. Wang, C. Sullards, D. Ringe, X. Cheng, R. A. Kahn
Date :  10 Sep 02  (Deposition) - 09 Oct 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.17
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Gtp-Binding, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. C. Amor, J. R. Horton, X. Zhu, Y. Wang, C. Sullards, D. Ringe, X. Cheng, R. A. Kahn
Structures Of Yeast Arf2 And Arl1: Distinct Roles For The N Terminus In The Structure And Function Of Arf Family Gtpases
J. Biol. Chem. V. 276 42477 2001
PubMed-ID: 11535602  |  Reference-DOI: 10.1074/JBC.M106660200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET3C
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymARL1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:27 , GLY A:28 , ALA A:29 , GLY A:30 , LYS A:31 , THR A:32 , THR A:33 , ASP A:68 , ASN A:127 , LYS A:128 , ASP A:130 , GLN A:131 , SER A:160 , ALA A:161 , ILE A:162BINDING SITE FOR RESIDUE GDP A 184
2AC2SOFTWAREASP B:27 , GLY B:28 , ALA B:29 , GLY B:30 , LYS B:31 , THR B:32 , THR B:33 , ASP B:68 , ASN B:127 , LYS B:128 , ASP B:130 , GLN B:131 , SER B:160 , ALA B:161 , ILE B:162BINDING SITE FOR RESIDUE GDP B 201

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:81 -B:81

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1MOZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARFPS51417 small GTPase Arf family profile.ARL1_YEAST12-178
 
  2A:12-178
B:12-178
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARFPS51417 small GTPase Arf family profile.ARL1_YEAST12-178
 
  1A:12-178
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARFPS51417 small GTPase Arf family profile.ARL1_YEAST12-178
 
  1-
B:12-178

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YBR164C1YBR164C.1II:568421-567870552ARL1_YEAST1-1831832A:2-183 (gaps)
B:2-183 (gaps)
182
182

(-) 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:178
 aligned with ARL1_YEAST | P38116 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:182
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  
           ARL1_YEAST     2 GNIFSSMFDKLWGSNKELRILILGLDGAGKTTILYRLQIGEVVTTKPTIGFNVETLSYKNLKLNVWDLGGQTSIRPYWRCYYADTAAVIFVVDSTDKDRMSTASKELHLMLQEEELQDAALLVFANKQDQPGALSASEVSKELNLVELKDRSWSIVASSAIKGEGITEGLDWLIDVIKEEQL 183
               SCOP domains d1moza_ A: ADP-ribosylation factor                                                                                                                                                     SCOP domains
               CATH domains 1mozA00 A:2-183 P-loop containing nucleotide triphosphate hydrolases                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.....eeeeeeee...hhhhhhhhh...eeeee.......eeeeee..eeeeeeee.----...hhhhh...eeeeeeeee.....hhhhhhhhhhhhh........eeeeeee........hhhhhhhhh.........eeeeeehhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------ARF  PDB: A:12-178 UniProt: 12-178                                                                                                                                     ----- PROSITE
               Transcript 1 Exon 1.1  PDB: A:2-183 (gaps) UniProt: 1-183 [INCOMPLETE]                                                                                                                              Transcript 1
                 1moz A   2 GNIFSSMFDKLWGSNKELRILILGLDGAGKTTILYRLQIGEVVTTKPTIGFNVETLSYKNLKLNVWDLG----IRPYWRCYYADTAAVIFVVDSTDKDRMSTASKELHLMLQEEELQDAALLVFANKQDQPGALSASEVSKELNLVELKDRSWSIVASSAIKGEGITEGLDWLIDVIKEEQL 183
                                    11        21        31        41        51        61        |-   |    81        91       101       111       121       131       141       151       161       171       181  
                                                                                               70   75                                                                                                            

Chain B from PDB  Type:PROTEIN  Length:178
 aligned with ARL1_YEAST | P38116 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:182
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  
           ARL1_YEAST     2 GNIFSSMFDKLWGSNKELRILILGLDGAGKTTILYRLQIGEVVTTKPTIGFNVETLSYKNLKLNVWDLGGQTSIRPYWRCYYADTAAVIFVVDSTDKDRMSTASKELHLMLQEEELQDAALLVFANKQDQPGALSASEVSKELNLVELKDRSWSIVASSAIKGEGITEGLDWLIDVIKEEQL 183
               SCOP domains d1mozb_ B: ADP-ribosylation factor                                                                                                                                                     SCOP domains
               CATH domains 1mozB00 B:2-183 P-loop containing nucleotide triphosphate hydrolases                                                                                                                   CATH domains
           Pfam domains (1) ---Arf-1mozB01 B:5-178                                                                                                                                                           ----- Pfam domains (1)
           Pfam domains (2) ---Arf-1mozB02 B:5-178                                                                                                                                                           ----- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhh.....eeeeeeee...hhhhhhhhh...eeeee.......eeeeee..eeeeeeee.----...........eeeeeeeee.....hhhhhhhhhhhhh........eeeeeee........hhhhhhhhh.........eeeeeehhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------ARF  PDB: B:12-178 UniProt: 12-178                                                                                                                                     ----- PROSITE
               Transcript 1 Exon 1.1  PDB: B:2-183 (gaps) UniProt: 1-183 [INCOMPLETE]                                                                                                                              Transcript 1
                 1moz B   2 GNIFSSMFDKLWGSNKELRILILGLDGAGKTTILYRLQIGEVVTTKPTIGFNVETLSYKNLKLNVWDLG----IRPYWRCYYADTAAVIFVVDSTDKDRMSTASKELHLMLQEEELQDAALLVFANKQDQPGALSASEVSKELNLVELKDRSWSIVASSAIKGEGITEGLDWLIDVIKEEQL 183
                                    11        21        31        41        51        61        |-   |    81        91       101       111       121       131       141       151       161       171       181  
                                                                                               70   75                                                                                                            

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ARL1_YEAST | P38116)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0043001    Golgi to plasma membrane protein transport    The directed movement of proteins from the Golgi to the plasma membrane in transport vesicles that move from the trans-Golgi network to the plasma membrane.
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:0000042    protein targeting to Golgi    The process of directing proteins towards the Golgi; usually uses signals contained within the protein.
    GO:0006623    protein targeting to vacuole    The process of directing proteins towards the vacuole, 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:0034976    response to endoplasmic reticulum stress    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
    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.
    GO:0016192    vesicle-mediated transport    A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.

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(-) Related Entries Specified in the PDB File

1hur HUMAN ADP-RIBOSYLATION FACTOR 1 COMPLEXED WITH GDP, FULL LENGTH NON-MYRISTOYLATE
1rrf NON-MYRISTOYLATED RAT ADP-RIBOSYLATION FACTOR-1 COMPLEXED WITH GDP, MONOMERIC CRYSTAL FORM