1U8Z - JenaLib

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Title :   CRYSTAL STRUCTURES OF RAL-GPPNHP AND RAL-GDP REVEAL TWO NOVEL BINDING SITES THAT ARE ALSO PRESENT IN RAS AND RAP

Authors :   N. I. Nicely, J. Kosak, V. De Serrano, C. Mattos

Date :   09 Aug 04 (Deposition) - 23 Nov 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Ral, Gnp, Gtp, Gmppnp, Gppnhp, Gdp, Gtpase, Ras, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. I. Nicely, J. Kosak, V. De Serrano, C. Mattos
Crystal Structures Of Ral-Gppnhp And Ral-Gdp Reveal Two Binding Sites That Are Also Present In Ras And Rap
Structure V. 12 2025 2004
PubMed-ID: 15530367 | Reference-DOI: 10.1016/J.STR.2004.08.011
(for further references see the PDB file header)

Molecule 1 - RAS-RELATED PROTEIN RAL-A
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PAT
	Expression System Strain	:	ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RALA, RAL-A, RAL
	Organism Common	:	COTTON-TOP TAMARIN
	Organism Scientific	:	SAGUINUS OEDIPUS
	Organism Taxid	:	9490

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:28 , GDP A:201 , HOH A:411 , HOH A:433 , HOH A:434 , HOH A:435	BINDING SITE FOR RESIDUE MG A 301
2	AC2	SOFTWARE	SER B:28 , GDP B:202 , HOH B:724 , HOH B:740 , HOH B:758 , HOH B:759	BINDING SITE FOR RESIDUE MG B 302
3	AC3	SOFTWARE	GLY A:24 , VAL A:25 , GLY A:26 , LYS A:27 , SER A:28 , ALA A:29 , PHE A:39 , GLU A:41 , ASN A:127 , LYS A:128 , ASP A:130 , LEU A:131 , SER A:157 , ALA A:158 , LYS A:159 , MG A:301 , HOH A:411 , HOH A:415 , HOH A:419 , HOH A:422 , HOH A:433 , HOH A:435 , HOH A:444 , HOH A:461 , HOH A:549	BINDING SITE FOR RESIDUE GDP A 201
4	AC4	SOFTWARE	GLY B:24 , VAL B:25 , GLY B:26 , LYS B:27 , SER B:28 , ALA B:29 , PHE B:39 , GLU B:41 , ASN B:127 , LYS B:128 , ASP B:130 , LEU B:131 , SER B:157 , ALA B:158 , LYS B:159 , MG B:302 , HOH B:705 , HOH B:706 , HOH B:711 , HOH B:720 , HOH B:724 , HOH B:738 , HOH B:740 , HOH B:759 , HOH B:803 , HOH B:872	BINDING SITE FOR RESIDUE GDP B 202

(no "SS Bond" information available for 1U8Z)

(no "Cis Peptide Bond" information available for 1U8Z)

(no "SAP(SNP)/Variant" information available for 1U8Z)

(no "PROSITE Motif" information available for 1U8Z)

(no "Exon" information available for 1U8Z)

Asymmetric Unit

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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:165
 aligned with RALA_SAGOE | P63320 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:168
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170        
           RALA_SAGOE    11 SLALHKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQIDILDTAGQEDYAAIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSVEEAKNRADQWNVNYVETSAKTRANVDKVFFDLMREIRAR 178
               SCOP domains d1u8za_ A: Ras-related protein RalA                                                                                                                                      SCOP domains
               CATH domains 1u8zA00 A:11-178 P-loop containing nucleotide triphosphate hy   drolases                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee.....hhhhhhhhhhhh...........eeeeeeeee..eeeeeeeee...---hhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeeehhhhhhhh..hhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1u8z A  11 SLALHKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQIDILDTAG---YAAIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSVEEAKNRADQWNVNYVETSAKTRANVDKVFFDLMREIRAR 178
                                    20        30        40        50        60        70|   |   80        90       100       110       120       130       140       150       160       170        
                                                                                       71  75

Chain B from PDB  Type:PROTEIN  Length:163
 aligned with RALA_SAGOE | P63320 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:167
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       
           RALA_SAGOE    12 LALHKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQIDILDTAGQEDYAAIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSVEEAKNRADQWNVNYVETSAKTRANVDKVFFDLMREIRAR 178
               SCOP domains d1u8zb_ B: Ras-related protein RalA                                                                                                                                     SCOP domains
               CATH domains 1u8zB00 B:12-178 P-loop containing nucleotide triphosphate     hydrolases                                                                                               CATH domains
           Pfam domains (1) ----Ras-1u8zB01 B:16-177                                                                                                                                              - Pfam domains (1)
           Pfam domains (2) ----Ras-1u8zB02 B:16-177                                                                                                                                              - Pfam domains (2)
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhh...........eeeeeeeee..eeeeeeeee..----.hhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhh..hhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u8z B  12 LALHKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQIDILDTA----YAAIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSVEEAKNRADQWNVNYVETSAKTRANVDKVFFDLMREIRAR 178
                                    21        31        41        51        61        |-   |    81        91       101       111       121       131       141       151       161       171       
                                                                                     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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: G proteins (693)

Protein domain: Ras-related protein RalA (8)

Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490] (3)

1a	d1u8za_	A:
1b	d1u8zb_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Cotton-top tamarin (Saguinus oedipus) (3)

1a	1u8zA00	A:11-178
1b	1u8zB00	B:12-178

Asymmetric Unit

Clans(

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Families(

)

Organisms( (-)

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Clan: P-loop_NTPase (1112)

Family: Ras (176)

Saguinus oedipus (Cotton-top tamarin) (3)

1a	Ras-1u8zB01	B:16-177
1b	Ras-1u8zB02	B:16-177

Asymmetric Unit(hide GO term definitions)

Chain A,B (RALA_SAGOE | P63320)

molecular function
	GO:0031755	Edg-2 lysophosphatidic acid receptor binding	Interacting selectively and non-covalently with an Edg-2 lysophosphatidic acid receptor.
	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:0007265	Ras protein signal transduction	A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	GO:0000910	cytokinesis	The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells.
	GO:0006887	exocytosis	A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
	GO:0051665	membrane raft localization	Any process in which membrane rafts are transported to, or maintained in, a specific location. Membrane rafts are small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes.
	GO:0017157	regulation of exocytosis	Any process that modulates the frequency, rate or extent of exocytosis.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	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.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0032154	cleavage furrow	The cleavage furrow is a plasma membrane invagination at the cell division site. The cleavage furrow begins as a shallow groove and eventually deepens to divide the cytoplasm.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0030496	midbody	A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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Description

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Ligands, Modified Residues, Ions (2, 4)

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