2IQY - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   RAT PHOSPHATIDYLETHANOLAMINE-BINDING PROTEIN

Authors :   Y. Kim, G. Joachimiak, G. L. Heil, S. Koide, A. Joachimiak

Date :   14 Oct 06 (Deposition) - 25 Sep 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym./Biol. Unit : A

Keywords :   Alpha-Beta, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kim, G. Joachimiak, G. L. Heil, S. Koide, A. Joachimiak
Crystal Structure Of Rat Phosphatidylethanolamine-Binding Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PHOSPHATIDYLETHANOLAMINE-BINDING PROTEIN 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	PEBP-1, HCNPPP, 23 KDA MORPHINE-BINDING PROTEIN, P23K

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	CL	1	Ligand/Ion	CHLORIDE ION

(no "Site" information available for 2IQY)

(no "SS Bond" information available for 2IQY)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:73	-	Pro A:74
2	Arg A:82	-	Glu A:83

(no "SAP(SNP)/Variant" information available for 2IQY)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PBP	PS01220	Phosphatidylethanolamine-binding protein family signature.	PEBP1_RAT	64-86	1	A:64-86

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000001500	1	ENSRNOE00000009897	chr12:40491378-40491580	203	PEBP1_RAT	1-45	45	1	A:1-45	45
1.2	ENSRNOT00000001500	2	ENSRNOE00000009898	chr12:40492518-40492627	110	PEBP1_RAT	46-82	37	1	A:46-82	37
1.3	ENSRNOT00000001500	3	ENSRNOE00000284299	chr12:40492907-40493007	101	PEBP1_RAT	82-116	35	1	A:82-116	35
1.4	ENSRNOT00000001500	4	ENSRNOE00000009900	chr12:40494956-40495590	635	PEBP1_RAT	116-187	72	1	A:116-187	72

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:190
 aligned with PEBP1_RAT | P31044 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:190
                               1                                                                                                                                                                                          
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187
            PEBP1_RAT     - ---MAADISQWAGPLSLQEVDEPPQHALRVDYGGVTVDELGKVLTPTQVMNRPSSISWDGLDPGKLYTLVLTDPDAPSRKDPKFREWHHFLVVNMKGNDISSGTVLSEYVGSGPPKDTGLHRYVWLVYEQEQPLNCDEPILSNKSGDNRGKFKVESFRKKYHLGAPVAGTCFQAEWDDSVPKLHDQLAGK 187
               SCOP domains d2iqya_ A: automated matches                                                                                                                                                                   SCOP domains
               CATH domains 2iqyA00 A:-2-187 Phosphatidylethanolamine-binding Protein;                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh....hhhhh.....ee.eee..........ee.hhhhhh....eee........eeeeeeee.............eeeeeeeeee..hhhhheeee.............eeeeeeeee.......................hhhhhhhhh......eeeeeee....hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------PBP  PDB: A:64-86      ----------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) ---Exon 1.1  PDB: A:1-45 UniProt: 1-45          Exon 1.2  PDB: A:46-82 UniProt: 46-82---------------------------------Exon 1.4  PDB: A:116-187 UniProt: 116-187                                Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------Exon 1.3  PDB: A:82-116            ----------------------------------------------------------------------- Transcript 1 (2)
                 2iqy A  -2 SNAMAADISQWAGPLSLQEVDEPPQHALRVDYGGVTVDELGKVLTPTQVMNRPSSISWDGLDPGKLYTLVLTDPDAPSRKDPKFREWHHFLVVNMKGNDISSGTVLSEYVGSGPPKDTGLHRYVWLVYEQEQPLNCDEPILSNKSGDNRGKFKVESFRKKYHLGAPVAGTCFQAEWDDSVPKLHDQLAGK 187
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187

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

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: All beta proteins (24004)

Fold: PEBP-like (18)

Superfamily: PEBP-like (18)

Family: Phosphatidylethanolamine binding protein (12)

Protein domain: automated matches (4)

Norway rat (Rattus norvegicus) [TaxId: 10116] (2)

d2iqya_

Asymmetric/Biological Unit

Classes(

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Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Phosphatidylethanolamine-binding Protein (16)

Homologous Superfamily: Phosphatidylethanolamine-binding Protein; (16)

Norway rat (Rattus norvegicus) (2)

2iqyA00

A:-2-187

(no "Pfam Domain" information available for 2IQY)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PEBP1_RAT | P31044)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0019900	kinase binding	Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	GO:0051019	mitogen-activated protein kinase binding	Interacting selectively and non-covalently with a mitogen-activated protein kinase.
	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:0030414	peptidase inhibitor activity	Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
	GO:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
	GO:0004867	serine-type endopeptidase inhibitor activity	Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
	GO:0000165	MAPK cascade	An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
	GO:0007568	aging	A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
	GO:0042755	eating behavior	The specific behavior of an organism relating to the intake of food, any substance (usually solid) that can be metabolized by an organism to give energy and build tissue.
	GO:0021766	hippocampus development	The progression of the hippocampus over time from its initial formation until its mature state.
	GO:0043409	negative regulation of MAPK cascade	Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the MAPKKK cascade.
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0010466	negative regulation of peptidase activity	Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
	GO:0001933	negative regulation of protein phosphorylation	Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
	GO:0060409	positive regulation of acetylcholine metabolic process	Any process that increases the rate, frequency or extent of the chemical reactions and pathways involving acetylcholine, the acetic acid ester of the organic base choline. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues.
	GO:0043950	positive regulation of cAMP-mediated signaling	Any process which activates, maintains or increases the frequency, rate or extent of cAMP-mediated signaling, a series of molecular signals in which a cell uses cyclic AMP to convert an extracellular signal into a response.
	GO:0045840	positive regulation of mitotic nuclear division	Any process that activates or increases the frequency, rate or extent of mitosis.
	GO:0001505	regulation of neurotransmitter levels	Any process that modulates levels of neurotransmitter.
	GO:0002026	regulation of the force of heart contraction	Any process that modulates the extent of heart contraction, changing the force with which blood is propelled.
	GO:0014823	response to activity	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 an activity stimulus.
	GO:0051591	response to cAMP	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 cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
	GO:0051592	response to calcium ion	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 calcium ion stimulus.
	GO:0051412	response to corticosterone	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 corticosterone stimulus. Corticosterone is a 21 carbon steroid hormone of the corticosteroid type, produced in the cortex of the adrenal glands. In many species, corticosterone is the principal glucocorticoid, involved in regulation of fuel metabolism, immune reactions, and stress responses.
	GO:0042493	response to drug	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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0051602	response to electrical 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 an electrical stimulus.
	GO:0045471	response to ethanol	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 an ethanol stimulus.
	GO:0009408	response to heat	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 heat stimulus, a temperature stimulus above the optimal temperature for that organism.
	GO:0014070	response to organic cyclic compound	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 an organic cyclic compound stimulus.
	GO:0010033	response to organic substance	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 an organic substance stimulus.
	GO:0010243	response to organonitrogen compound	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 an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.
	GO:0006979	response to oxidative stress	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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	GO:0009636	response to toxic substance	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 toxic stimulus.
	GO:0009611	response to wounding	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 indicating damage to the organism.
	GO:0048240	sperm capacitation	A process required for sperm to reach fertilization competence. Sperm undergo an incompletely understood series of morphological and molecular maturational processes, termed capacitation, involving, among other processes, protein tyrosine phosphorylation and increased intracellular calcium.
	GO:0007286	spermatid development	The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure.
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:0045177	apical part of cell	The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue.
	GO:0043679	axon terminus	Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal button is a specialized region of it.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005741	mitochondrial outer membrane	The outer, i.e. cytoplasm-facing, lipid bilayer 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:0043209	myelin sheath	An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
	GO:0043005	neuron projection	A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	GO:0005791	rough endoplasmic reticulum	The rough (or granular) endoplasmic reticulum (ER) has ribosomes adhering to the outer surface; the ribosomes are the site of translation of the mRNA for those proteins which are either to be retained within the cisternae (ER-resident proteins), the proteins of the lysosomes, or the proteins destined for export from the cell. Glycoproteins undergo their initial glycosylation within the cisternae.
	GO:0008021	synaptic vesicle	A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.

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	Cis Peptide Bonds
		Ala A:73 - Pro A:74	[ RasMol ]
		Arg A:82 - Glu A:83	[ RasMol ]

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	PEBP1_RAT \| P31044	:	2iqx

2iqx	RAT PHOSPHATIDYLETHANOLAMINE-BINDING PROTEIN CONTAINING THE S153E MUTATION IN THE COMPLEX WITH O-PHOSPHORYLETHANOLAMINE

Description

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Ligands, Modified Residues, Ions (2, 2)

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SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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Exons (4, 4)

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