1KSJ - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   COMPLEX OF ARL2 AND PDE DELTA, CRYSTAL FORM 2 (SEMET)

Authors :   M. Hanzal-Bayer, L. Renault, P. Roversi, A. Wittinghofer, R. C. Hillig

Date :   13 Jan 02 (Deposition) - 08 May 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym./Biol. Unit : A,B

Keywords :   Small Gtpase, Small Gtp-Binding Protein, Arf Family, Effector Molecule, Immunoglobuline-Like Fold, Gdi, Signaling Protein- Hydrolase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Hanzal-Bayer, L. Renault, P. Roversi, A. Wittinghofer, R. C. Hilli
The Complex Of Arl2-Gtp And Pde Delta: From Structure To Function
Embo J. V. 21 2095 2002
PubMed-ID: 11980706 | Reference-DOI: 10.1093/EMBOJ/21.9.2095
(for further references see the PDB file header)

Molecule 1 - ARF-LIKE PROTEIN 2
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX KG
	Expression System Strain	:	B834
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ARL2
	Mutation	:	YES
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - RETINAL ROD RHODOPSIN-SENSITIVE CGMP 3',5'-CYCLIC PHOSPHODIESTERASE DELTA-SUBUNIT
	Chains	:	B
	EC Number	:	3.1.4.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	B834
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PDE6D OR PDED
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GMP-PDE DELTA, P17 PROTEIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (7, 11)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CME	2	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE
3	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
4	GTP	1	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
5	MG	1	Ligand/Ion	MAGNESIUM ION
6	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
7	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:26 , LYS A:29 , THR A:47 , GLY A:69 , GDP A:201 , MG A:205 , HOH A:239 , HOH A:240 , HOH A:245	BINDING SITE FOR RESIDUE PO4 A 202
2	AC2	SOFTWARE	THR A:30 , THR A:47 , GDP A:201 , PO4 A:202 , GTP A:203 , HOH A:239 , HOH A:240	BINDING SITE FOR RESIDUE MG A 205
3	AC3	SOFTWARE	LEU A:24 , VAL A:91 , ASP A:92 , ASP A:95 , MSE A:99 , CYS A:102 , HOH A:247 , HOH A:248	BINDING SITE FOR RESIDUE BME A 236
4	AC4	SOFTWARE	LEU A:24 , ASP A:25 , ASN A:26 , ALA A:27 , GLY A:28 , LYS A:29 , THR A:30 , THR A:31 , ILE A:44 , ASN A:125 , LYS A:126 , ASP A:128 , SER A:158 , ALA A:159 , VAL A:160 , PO4 A:202 , MG A:205 , HOH A:239 , HOH A:240 , HOH A:266 , GLY B:84 , CME B:86	BINDING SITE FOR RESIDUE GDP A 201
5	AC5	SOFTWARE	ASP A:25 , ASN A:26 , ALA A:27 , GLY A:28 , LYS A:29 , THR A:30 , THR A:31 , ILE A:44 , PRO A:46 , THR A:47 , GLY A:69 , ASN A:125 , LYS A:126 , ASP A:128 , LEU A:129 , SER A:158 , ALA A:159 , VAL A:160 , MG A:205 , HOH A:239 , HOH A:240 , HOH A:245 , TYR B:81 , GLY B:84 , CME B:86	BINDING SITE FOR RESIDUE GTP A 203

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

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

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

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

Asymmetric/Biological Unit (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3a	ENST00000287600	3a	ENSE00001829481	chr2:232646019-232645775	245	PDE6D_HUMAN	1-17	17	1	B:2-17	16
1.5b	ENST00000287600	5b	ENSE00001029423	chr2:232603898-232603810	89	PDE6D_HUMAN	17-47	31	1	B:17-47	31
1.6a	ENST00000287600	6a	ENSE00001029425	chr2:232602848-232602723	126	PDE6D_HUMAN	47-89	43	1	B:47-89	43
1.7	ENST00000287600	7	ENSE00001029421	chr2:232602002-232601897	106	PDE6D_HUMAN	89-124	36	1	B:89-124 (gaps)	36
1.9b	ENST00000287600	9b	ENSE00001872609	chr2:232597743-232597135	609	PDE6D_HUMAN	124-150	27	1	B:124-150	27

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:165
 aligned with ARL2_MOUSE | Q9D0J4 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:165
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174     
           ARL2_MOUSE    15 RELRLLMLGLDNAGKTTILKKFNGEDVDTISPTLGFNIKTLEHRGFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADRQRMQDCQRELQSLLVEERLAGATLLIFANKQDLPGALSCNAIQEALELDSIRSHHWRIQGCSAVTGEDLLPGIDWLLDDISSR 179
               SCOP domains d1ksja_ A: ADP-ribosylation factor                                                                                                                                    SCOP domains
               CATH domains 1ksjA00 A:15-179 P-loop containing nucleotide triphosphate hydrolases                                                                                                 CATH domains
               Pfam domains Arf-1ksjA01 A:15-176                                                                                                                                              --- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhh............eeeeeeee..eeeeeeee..hhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhhh........eeeeeee........hhhhhhhhh.........eeeee........hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ksj A  15 RELRLLmLGLDNAGKTTILKKFNGEDVDTISPTLGFNIKTLEHRGFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADRQRmQDCQRELQSLLVEERLAGATLLIFANKQDLPGALScNAIQEALELDSIRSHHWRIQGCSAVTGEDLLPGIDWLLDDISSR 179
                                  | 24        34        44        54        64        74        84        94    |  104       114       124       134|      144       154       164       174     
                                 21-MSE                                                                        99-MSE                             135-CME

Chain B from PDB  Type:PROTEIN  Length:141
 aligned with PDE6D_HUMAN | O43924 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:149
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         
          PDE6D_HUMAN     2 SAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV 150
               SCOP domains d1ksjb_ B: GMP-PDE delta                                                                                                                              SCOP domains
               CATH domains 1ksjB00 B:2-150                                                                                                                                       CATH domains
               Pfam domains -----GMP_PDE_delta-1ksjB01 B:7-150                                                                                                                    Pfam domains
         Sec.struct. author hhhhhhhhhhhhheeeeeeeeee....eeeee...........eeeeehhhhhh...eeeeeeeee...eeeeeeeeeeee..eeeeeeeeeeeee...eeeeeeeee.--------........eeeeeeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a       -----------------------------Exon 1.6a  PDB: B:47-89 UniProt: 47-89     ----------------------------------Exon 1.9b  PDB: B:124-150   Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.5b  PDB: B:17-47        -----------------------------------------Exon 1.7  PDB: B:89-124 (gaps)      -------------------------- Transcript 1 (2)
                 1ksj B   2 SAKDERAREILRGFKLNWmNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQmEKFRLEQKVYFKGQcLEEWFFEFGFVIPNSTNTWQSLIE--------PASVLTGNVIIETKFFDDDLLVSTSRVRLFYV 150
                                    11        21        31        41        51        61        71        81    |   91       101        |-       121       131       141         
                                             20-MSE                                             71-MSE         86-CME                 110      119

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/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Arf (26)

Mus musculus (Mouse) (3)

Arf-1ksjA01

A:15-176

Clan: no clan defined [family: GMP_PDE_delta] (3)

Family: GMP_PDE_delta (3)

Homo sapiens (Human) (3)

GMP_PDE_delta-1ksjB01

B:7-150

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ARL2_MOUSE | Q9D0J4)

molecular function
	GO:0019003	GDP binding	Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate.
	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:0070830	bicellular tight junction assembly	The aggregation, arrangement and bonding together of a set of components to form a tight junction, an occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet.
	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:0051457	maintenance of protein location in nucleus	Any process in which a protein is maintained in the nucleus and prevented from moving elsewhere. These include sequestration within the nucleus, protein stabilization to prevent transport elsewhere and the active retrieval of proteins that escape the nucleus.
	GO:0034260	negative regulation of GTPase activity	Any process that stops or reduces the rate of GTP hydrolysis by a GTPase.
	GO:0010811	positive regulation of cell-substrate adhesion	Any process that increases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules.
	GO:0031116	positive regulation of microtubule polymerization	Any process that activates or increases the frequency, rate or extent of microtubule polymerization.
	GO:0031113	regulation of microtubule polymerization	Any process that modulates the frequency, rate or extent of microtubule polymerization.
	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:0005813	centrosome	A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	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: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:0016328	lateral plasma membrane	The portion of the plasma membrane at the lateral side of the cell. In epithelial cells, lateral plasma membranes are on the sides of cells which lie at the interface of adjacent cells.
	GO:0005815	microtubule organizing center	An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
	GO:0005758	mitochondrial intermembrane space	The region between the inner and outer lipid bilayers of the mitochondrial envelope.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain B (PDE6D_HUMAN | O43924)

molecular function
	GO:0004114	3',5'-cyclic-nucleotide phosphodiesterase activity	Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate.
	GO:0005095	GTPase inhibitor activity	Stops, prevents or reduces the activity of any enzyme that catalyzes the hydrolysis of GTP to GDP and orthophosphate.
	GO:0017137	Rab GTPase binding	Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases.
	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:0034260	negative regulation of GTPase activity	Any process that stops or reduces the rate of GTP hydrolysis by a GTPase.
	GO:0050896	response to stimulus	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 stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
	GO:0007601	visual perception	The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.
cellular component
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	GO:0030659	cytoplasmic vesicle membrane	The lipid bilayer surrounding a cytoplasmic vesicle.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ksj)

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	PDE6D_HUMAN \| O43924
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1doa	STRUCTURE OF THE RHO FAMILY GTP-BINDING PROTEIN CDC42 IN COMPLEX WITH THE MULTIFUNCTIONAL REGULATOR RHOGDI
1fzq	CRYSTAL STRUCTURE OF MURINE ARL3-GDP
1ksg	COMPLEX OF ARL2 AND PDE DELTA, CRYSTAL FORM 1
1ksh	COMPLEX OF ARL2 AND PDE DELTA, CRYSTAL FORM 2 (NATIVE)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 11)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (5, 5)

Sequences/Alignments

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SCOP Domains (2, 2)

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Pfam Domains (2, 2)

Gene Ontology (33, 37)

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