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NMR Structure - model 1

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NMR Structure - model 1 (Jmol Viewer)

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Description

Title :   SIDEROCALIN Q83 REVEALS A DUAL LIGAND BINDING MODE

Authors :   N. Coudevylle, M. Hoetzinger, L. Geist, G. Kontaxis, K. Bister, R. Konr

Date :   07 Apr 11 (Deposition) - 22 Feb 12 (Release) - 22 Feb 12 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)
NMR Structure *: A  (1x)

Keywords :   Lipocalin, Siderocalin, Enterobactin, Arachidonic Acid, Lipid Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Coudevylle, M. Hoetzinger, L. Geist, G. Kontaxis, M. Hartl, K. Bister, R. Konrat
Lipocalin Q83 Reveals A Dual Ligand Binding Mode With Potential Implications For The Functions Of Siderocalins
Biochemistry V. 50 9192 2011
PubMed-ID: 21951132 | Reference-DOI: 10.1021/BI201115Q

Compounds

Molecule 1 - EXTRACELLULAR FATTY ACID-BINDING PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PET3D
	Expression System Vector Type	:	VECTOR
	Organism Common	:	JAPANESE QUAIL
	Organism Scientific	:	COTURNIX JAPONICA
	Organism Taxid	:	93934
	Synonym	:	EX-FABP, LIPOCALIN Q83

Structural Features

Chains, Units

		1
NMR Structure (20x)	:	A
NMR Structure * (1x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 3)

NMR Structure (3, 3)

No.	Name	Count	Type	Full Name
1	ACD	1	Ligand/Ion	ARACHIDONIC ACID
2	EB4	1	Ligand/Ion	N,N',N''-[(3S,7S,11S)-2,6,10-TRIOXO-1,5,9-TRIOXACYCLODODECANE-3,7,11-TRIYL]TRIS(2,3-DIHYDROXYBENZAMIDE)
3	GA	1	Ligand/Ion	GALLIUM (III) ION

NMR Structure * (2, 2)

No.	Name	Count	Type	Full Name
1	ACD	1	Ligand/Ion	ARACHIDONIC ACID
2	EB4	1	Ligand/Ion	N,N',N''-[(3S,7S,11S)-2,6,10-TRIOXO-1,5,9-TRIOXACYCLODODECANE-3,7,11-TRIYL]TRIS(2,3-DIHYDROXYBENZAMIDE)
3	GA	-1	Ligand/Ion	GALLIUM (III) ION

Sites (3, 3)

NMR Structure (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:25 , MET A:32 , TYR A:51 , VAL A:53 , TRP A:62 , LYS A:83 , ARG A:102 , LEU A:109 , MET A:111 , GA A:201 , ACD A:300	BINDING SITE FOR RESIDUE EB4 A 200
2	AC2	SOFTWARE	EB4 A:200	BINDING SITE FOR RESIDUE GA A 201
3	AC3	SOFTWARE	TRP A:13 , ALA A:37 , ILE A:39 , PHE A:41 , VAL A:49 , SER A:50 , TYR A:51 , VAL A:85 , TYR A:92 , ILE A:98 , ARG A:113 , TYR A:115 , EB4 A:200	BINDING SITE FOR RESIDUE ACD A 300

SS Bonds (1, 1)

NMR Structure

No.	Residues
1	A:59	-	A:152

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2LBV)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (1, 1)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIPOCALIN	PS00213	Lipocalin signature.	EXFAB_COTJA	26-37	1	A:5-16

NMR Structure * (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIPOCALIN	PS00213	Lipocalin signature.	EXFAB_COTJA	26-37	1	A:5-16

Exons (0, 0)

(no "Exon" information available for 2LBV)

Sequences/Alignments

NMR Structure

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
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Chain A from PDB  Type:PROTEIN  Length:157
 aligned with EXFAB_COTJA | Q9I9P7 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:157
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       
          EXFAB_COTJA    22 ATVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDELKVSYAVPKPNGCRKWETTFKKTSDDGEVYYSEEAKKKVEVLDTDYKSYAVIYATRVKDGRTLHMMRLYSRSPEVSPAATAIFRKLAGERNYTDEMVAMLPRQEECTVDEV 178
               SCOP domains d2lbva_ A: Lipocalin q83                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh..eeeeeee..hhhhhhhhh....eeeeeeeee..eeeeeeee......eeeeeeee.......eeee....eeeeeeee....eeeeeeee........eeeeee.....hhhhhhhhhhhhhhh..hhh.eee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----LIPOCALIN   --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2lbv A   1 MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDELKVSYAVPKPNGCRKWETTFKKTSDDGEVYYSEEAKKKVEVLDTDYKSYAVIYATRVKDGRTLHMMRLYSRSPEVSPAATAIFRKLAGERNYTDEMVAMLPRQEECTVDEV 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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)

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Lipocalins (514)

Superfamily: Lipocalins (514)

Family: Retinol binding protein-like (261)

Protein domain: Lipocalin q83 (3)

Coturnix japonica [TaxId: 93934] (2)

d2lbva_

CATH Domains (0, 0)

(no "CATH Domain" information available for 2LBV)

Pfam Domains (0, 0)

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

Gene Ontology (11, 11)

NMR Structure(hide GO term definitions)

Chain A (EXFAB_COTJA | Q9I9P7)

molecular function
	GO:0050544	arachidonic acid binding	Interacting selectively and non-covalently with arachidonic acid, a straight chain fatty acid with 20 carbon atoms and four double bonds per molecule. Arachidonic acid is the all-Z-(5,8,11,14)-isomer.
	GO:1903981	enterobactin binding	Interacting selectively and non-covalently with enterobactin.
	GO:0070538	oleic acid binding	Interacting selectively and non-covalently with oleic acid, the 18-carbon monounsaturated fatty acid (9Z)-octadec-9-enoic acid.
	GO:0036094	small molecule binding	Interacting selectively and non-covalently with a small molecule, any low molecular weight, monomeric, non-encoded molecule.
	GO:0005215	transporter activity	Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	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.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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Related Entries

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	EXFAB_COTJA \| Q9I9P7	:	1jzu 2kt4

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