2YFB - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   X-RAY STRUCTURE OF MCPS LIGAND BINDING DOMAIN IN COMPLEX WITH SUCCINATE

Authors :   J. A. Gavira, E. Pineda-Molina, T. Krell

Date :   05 Apr 11 (Deposition) - 18 Apr 12 (Release) - 10 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Chemoreceptor, Signal Transduction, Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Pineda-Molina, J. Reyes-Darias, J. Lacal, J. L. Ramos, J. M. Garcia-Ruiz, J. A. Gavira, T. Krell
Evidence For Chemoreceptors With Bimodular Ligand-Binding Regions Harboring Two Signal-Binding Sites.
Proc. Natl. Acad. Sci. Usa V. 109 18926 2012
PubMed-ID: 23112148 | Reference-DOI: 10.1073/PNAS.1201400109
(for further references see the PDB file header)

Molecule 1 - METHYL-ACCEPTING CHEMOTAXIS TRANSDUCER
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	LIGAND BINDING DOMAIN, RESIDUES 46-283
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	160488
	Strain	:	KT2440
	Synonym	:	MCPS

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 7)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	SIN	2	Ligand/Ion	SUCCINIC ACID
3	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:60 , ARG A:63 , ARG A:254 , THR A:258 , HOH A:2016 , HOH A:2017 , HOH A:2255 , HOH A:2260 , HOH A:2264 , GLN B:65	BINDING SITE FOR RESIDUE SIN A 500
2	AC2	SOFTWARE	MET A:137 , ASP A:138 , ARG A:183 , VAL A:186 , ARG A:187 , ILE A:190 , TYR A:236 , HOH A:2158	BINDING SITE FOR RESIDUE ACT A 501
3	AC3	SOFTWARE	HIS A:45 , PHE A:97 , LYS A:98 , SER A:99 , ASN A:102 , GLN A:275 , HOH A:2098	BINDING SITE FOR RESIDUE SO4 A1278
4	AC4	SOFTWARE	GLN A:65 , ARG B:60 , ARG B:63 , ARG B:254 , THR B:258 , HOH B:2018 , HOH B:2019 , HOH B:2214 , HOH B:2233	BINDING SITE FOR RESIDUE SIN B 500
5	AC5	SOFTWARE	ASP B:138 , ARG B:183 , VAL B:186 , ARG B:187 , TYR B:236 , HOH B:2144	BINDING SITE FOR RESIDUE ACT B 501
6	AC6	SOFTWARE	ARG A:124 , GLN A:125 , HOH A:2122 , HOH A:2138 , ARG B:124 , GLN B:125 , HOH B:2116 , HOH B:2118	BINDING SITE FOR RESIDUE SO4 B1278
7	AC7	SOFTWARE	HIS B:45 , PHE B:97 , LYS B:98 , SER B:99 , ASN B:102 , GLN B:275 , HOH B:2230	BINDING SITE FOR RESIDUE SO4 B1279

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

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

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HBM	PS51753	HBM domain profile.	MCPS_PSEPK	41-283	1	B:42-277

(no "Exon" information available for 2YFB)

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:235
 aligned with MCPS_PSEPK | Q88E10 from UniProtKB/Swiss-Prot  Length:639

    Alignment length:235
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272     
           MCPS_PSEPK    43 SNWMGDIGQLNKDLTDLRIARLQYMIANGDDTAAANTLAKLDAFSKQQAYLATTFKSPENVKLLGELGDTISAYKLSLNKMRQGYDATRAARVSMDSSAIRADQAMDALSQEVMARPEADSVRLAQYQLISKARQQLLQVRIDVRGYIAENSSANEQAALRQLDAALADTDNLKRQLPSEDARLQQFENAVLAYRDAVRQFRDAVANITTSRAEMTVQGADIVKRSDALYQIQLE 277
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE HBM  PDB: - UniProt: 41-283                                                                                                                                                                                                                 PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yfb A  43 GSHMGDIGQLNKDLTDLRIARLQYMIANGDDTAAANTLAKLDAFSKQQAYLATTFKSPENVKLLGELGDTISAYKLSLNKMRQGYDATRAARVSMDSSAIRADQAMDALSQEVMARPEADSVRLAQYQLISKARQQLLQVRIDVRGYIAENSSANEQAALRQLDAALADTDNLKRQLPSEDARLQQFENAVLAYRDAVRQFRDAVANITTSRAEMTVQGADIVKRSDALYQIQLE 277
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272

Chain B from PDB  Type:PROTEIN  Length:238
 aligned with MCPS_PSEPK | Q88E10 from UniProtKB/Swiss-Prot  Length:639

    Alignment length:238
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269        
           MCPS_PSEPK    40 IDRSNWMGDIGQLNKDLTDLRIARLQYMIANGDDTAAANTLAKLDAFSKQQAYLATTFKSPENVKLLGELGDTISAYKLSLNKMRQGYDATRAARVSMDSSAIRADQAMDALSQEVMARPEADSVRLAQYQLISKARQQLLQVRIDVRGYIAENSSANEQAALRQLDAALADTDNLKRQLPSEDARLQQFENAVLAYRDAVRQFRDAVANITTSRAEMTVQGADIVKRSDALYQIQLE 277
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -HBM  PDB: B:42-277 UniProt: 41-283                                                                                                                                                                                                            PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yfb B  40 VPRGSHMGDIGQLNKDLTDLRIARLQYMIANGDDTAAANTLAKLDAFSKQQAYLATTFKSPENVKLLGELGDTISAYKLSLNKMRQGYDATRAARVSMDSSAIRADQAMDALSQEVMARPEADSVRLAQYQLISKARQQLLQVRIDVRGYIAENSSANEQAALRQLDAALADTDNLKRQLPSEDARLQQFENAVLAYRDAVRQFRDAVANITTSRAEMTVQGADIVKRSDALYQIQLE 277
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269

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 '\|'

(no "SCOP Domain" information available for 2YFB)

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (MCPS_PSEPK | Q88E10)

molecular function
	GO:0004871	signal transducer activity	Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
	GO:0006935	chemotaxis	The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
	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.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2yfb)

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	MCPS_PSEPK \| Q88E10	:	2yfa

2yfa	X-RAY STRUCTURE OF MCPS LIGAND BINDING DOMAIN IN COMPLEX WITH MALATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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SCOP Domains (0, 0)

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Gene Ontology (6, 6)

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