1MR3 - JenaLib

Title :   SACCHAROMYCES CEREVISIAE ADP-RIBOSYLATION FACTOR 2 (SCARF2) COMPLEXED WITH GDP-3'P AT 1.6A RESOLUTION

Authors :   J. -C. Amor, J. R. Horton, X. Zhu, Y. Wang, C. Sullards, D. Ringe, X. Cheng

Date :   17 Sep 02 (Deposition) - 20 Nov 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym./Biol. Unit : F

Keywords :   Gtp-Binding, Gdp-3'Phosphate, Small Gtpase, Signal Transduction, Signaling Protein (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

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 20)

Sites (20, 20)

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR F:31 , G3D F:800 , HOH F:2078 , HOH F:2079 , HOH F:2080 , HOH F:2085	BINDING SITE FOR RESIDUE MG F 801
02	AC2	SOFTWARE	ASP F:26 , GLY F:27 , ALA F:28 , GLY F:29 , LYS F:30 , THR F:31 , THR F:32 , ASN F:126 , LYS F:127 , ASP F:129 , CYS F:159 , ALA F:160 , THR F:161 , MG F:801 , HOH F:2079 , HOH F:2085 , HOH F:2090 , HOH F:2091 , HOH F:2119 , HOH F:2139 , HOH F:2186 , HOH F:2189 , HOH F:2191 , HOH F:2193 , HOH F:2202 , HOH F:2233	BINDING SITE FOR RESIDUE G3D F 800
03	AC3	SOFTWARE	THR F:48 , ILE F:49 , GLY F:50 , PHE F:51 , SER F:135 , PDO F:2009 , EOH F:2047 , EDO F:2072 , HOH F:2098 , HOH F:2144	BINDING SITE FOR RESIDUE EDO F 2065
04	AC4	SOFTWARE	PRO F:152 , TRP F:153 , HOH F:2128	BINDING SITE FOR RESIDUE EDO F 2067
05	AC5	SOFTWARE	LYS F:16 , ASP F:93 , ASN F:95 , LEU F:130 , HOH F:2110 , HOH F:2187 , HOH F:2209	BINDING SITE FOR RESIDUE EDO F 2069
06	AC6	SOFTWARE	ASN F:112 , ASP F:114	BINDING SITE FOR RESIDUE EDO F 2071
07	AC7	SOFTWARE	THR F:48 , ARG F:75 , TRP F:78 , SER F:135 , PDO F:2009 , EOH F:2047 , EDO F:2065 , HOH F:2112 , HOH F:2222	BINDING SITE FOR RESIDUE EDO F 2072
08	AC8	SOFTWARE	THR F:32 , LYS F:36 , THR F:161 , HOH F:2089 , HOH F:2106 , HOH F:2189 , HOH F:2199	BINDING SITE FOR RESIDUE EDO F 2073
09	AC9	SOFTWARE	THR F:48 , ARG F:97 , GLU F:138 , HOH F:2185 , HOH F:2222 , HOH F:2260	BINDING SITE FOR RESIDUE EDO F 2074
10	BC1	SOFTWARE	ILE F:20 , LEU F:21 , THR F:64 , TYR F:81 , ASN F:84 , THR F:85 , HOH F:2195 , HOH F:2284	BINDING SITE FOR RESIDUE EDO F 2075
11	BC2	SOFTWARE	LYS F:36 , LYS F:38 , EDO F:2077	BINDING SITE FOR RESIDUE EDO F 2076
12	BC3	SOFTWARE	SER F:162 , GLY F:163 , GLU F:164 , EDO F:2076	BINDING SITE FOR RESIDUE EDO F 2077
13	BC4	SOFTWARE	ARG F:83 , GLU F:115 , ARG F:117 , ASN F:118 , HOH F:2162	BINDING SITE FOR RESIDUE GOL F 950
14	BC5	SOFTWARE	GLY F:50 , ASN F:52 , TRP F:66 , ASP F:67 , PDO F:2008 , PDO F:2009	BINDING SITE FOR RESIDUE GOL F 954
15	BC6	SOFTWARE	LEU F:25 , ASP F:93 , ASP F:96 , ARG F:99 , ILE F:100 , ALA F:103 , HOH F:2094	BINDING SITE FOR RESIDUE EOH F 2046
16	BC7	SOFTWARE	THR F:48 , PHE F:51 , ARG F:75 , TRP F:78 , SER F:135 , EDO F:2065 , EDO F:2072 , HOH F:2112 , HOH F:2222	BINDING SITE FOR RESIDUE EOH F 2047
17	BC8	SOFTWARE	GLN F:71 , GLN F:156 , GLU F:168 , HOH F:2188	BINDING SITE FOR RESIDUE EOH F 2048
18	BC9	SOFTWARE	ARG F:73 , HOH F:2190	BINDING SITE FOR RESIDUE EOH F 2049
19	CC1	SOFTWARE	ASN F:52 , GLU F:54 , VAL F:65 , TRP F:66 , ASP F:67 , GOL F:954 , HOH F:2078 , HOH F:2080	BINDING SITE FOR RESIDUE PDO F 2008
20	CC2	SOFTWARE	ASP F:72 , ARG F:73 , TRP F:78 , GOL F:954 , EDO F:2065 , EDO F:2072 , HOH F:2178	BINDING SITE FOR RESIDUE PDO F 2009

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (1, 1)

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 F from PDB  Type:PROTEIN  Length:177
 aligned with ARF2_YEAST | P19146 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:177
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       
           ARF2_YEAST     5 ASKLFSNLFGNKEMRILMVGLDGAGKTTVLYKLKLGEVITTIPTIGFNVETVQYKNISFTVWDVGGQDRIRSLWRHYYRNTEGVIFVIDSNDRSRIGEAREVMQRMLNEDELRNAVWLVFANKQDLPEAMSAAEITEKLGLHSIRNRPWFIQSTCATSGEGLYEGLEWLSNNLKNQS 181
               SCOP domains d1mr3f_ F: ADP-ribosylation factor                                                                                                                                                SCOP domains
               CATH domains 1mr3F00 F:5-181 P-loop containing nucleotide triphosphate hydrolases                                                                                                              CATH domains
               Pfam domains Arf-1mr3F01 F:5-177                                                                                                                                                          ---- Pfam domains
         Sec.struct. author ....hhhhhh...eeeeeeee...hhhhhhhhhh....eeeeee..eeeeeeee..eeeeeeee......hhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------ARF  PDB: F:11-177 UniProt: 11-177                                                                                                                                     ---- PROSITE
               Transcript 1 Exon 1.1  PDB: F:5-181 UniProt: 1-181 [INCOMPLETE]                                                                                                                                Transcript 1
                 1mr3 F   5 ASKLFSNLFGNKEMRILMVGLDGAGKTTVLYKLKLGEVITTIPTIGFNVETVQYKNISFTVWDVGGQDRIRSLWRHYYRNTEGVIFVIDSNDRSRIGEAREVMQRMLNEDELRNAVWLVFANKQDLPEAMSAAEITEKLGLHSIRNRPWFIQSTCATSGEGLYEGLEWLSNNLKNQS 181
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174

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 (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

Chain F (ARF2_YEAST | P19146)

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.
biological process
	GO:0016236	macroautophagy	The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure. Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Though once thought to be a purely non-selective process, it appears that some types of macroautophagy, e.g. macropexophagy, macromitophagy, may involve selective targeting of the targets to be degraded.
	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: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: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.

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