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Title :   CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE PUTATIVE HISTIDINE KINASE RPHK1S-Z16

Authors :   Z. Zhang, W. A. Hendrickson

Date :   24 Jan 10 (Deposition) - 05 May 10 (Release) - 11 Aug 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Pdc Fold, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Zhang, W. A. Hendrickson
Structural Characterization Of The Predominant Family Of Histidine Kinase Sensor Domains.
J. Mol. Biol. V. 400 335 2010
PubMed-ID: 20435045 | Reference-DOI: 10.1016/J.JMB.2010.04.049

Molecule 1 - PUTATIVE DIGUANYLATE CYCLASE (GGDEF) WITH PAS/PAC DOMAIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSMT3
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	EXTRACELLULAR DOMAIN (UNP RESIDUES 40-293)
	Gene	:	RPA3616
	Organism Scientific	:	RHODOPSEUDOMONAS PALUSTRIS
	Organism Taxid	:	1076

		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 (3, 12)

No.	Name	Count	Type	Full Name
1	CIT	2	Ligand/Ion	CITRIC ACID
2	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:137 , TYR A:139 , SER A:159 , ARG A:160 , THR A:161	BINDING SITE FOR RESIDUE MPD A 1
2	AC2	SOFTWARE	ARG A:57 , ARG A:242 , SER A:243 , ASP A:245 , GLY A:246 , HOH A:328	BINDING SITE FOR RESIDUE CIT A 294
3	AC3	SOFTWARE	LEU B:132 , ARG B:137 , TYR B:139 , SER B:159 , ARG B:160 , THR B:161	BINDING SITE FOR RESIDUE MPD B 2
4	AC4	SOFTWARE	ARG B:57 , ARG B:242 , SER B:243 , ASP B:245 , HOH B:305	BINDING SITE FOR RESIDUE CIT B 294

(no "SS Bond" information available for 3LIF)

Asymmetric Unit

No.	Residues
1	Lys A:127	-	Pro A:128
2	Gly A:155	-	Pro A:156
3	Trp A:221	-	Pro A:222
4	Asp A:245	-	Gly A:246
5	Val A:282	-	Leu A:283
6	Leu A:283	-	Ser A:284
7	Ser A:284	-	Gly A:285
8	Gly B:155	-	Pro B:156
9	Trp B:221	-	Pro B:222
10	Ser B:281	-	Val B:282

(no "SAP(SNP)/Variant" information available for 3LIF)

(no "PROSITE Motif" information available for 3LIF)

(no "Exon" information available for 3LIF)

Asymmetric 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:243
 aligned with Q6N3S7_RHOPA | Q6N3S7 from UniProtKB/TrEMBL  Length:644

    Alignment length:243
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282   
         Q6N3S7_RHOPA    43 DSHKIALAQSETEMRNLSHSLAEHATHTFQGADVVLDDIVSFMKWRPHPSPVFNERLRALADNLPQLSDVAILDADGQLTYASVKPVPALDNSDRSYFRYHRANDDHTLLITGPIQSRTSGVWVFVVSRRLETTDGKFFGVVVATIESEYFSTFYKTFDLGPGGSISLLHSDGRLLIQWPSLQTGRDMANMVLFQKALPRSPDGYYLTVSPFDGLTKYLAYRRVSRYPLVVTVARTEDSVLSG 285
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..eeeeeee.....eeee....ee......hhhhhhhhhh.....eeeeeee......eeeeeeeeee.....eeeeeeeeehhhhhhhhhh........eeeeee....eeeee...........hhhhhhhhhhh.eeeeeee......eeeeeeee.....eeeeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lif A  43 DSHKIALAQSETEmRNLSHSLAEHATHTFQGADVVLDDIVSFmKWRPHPSPVFNERLRALADNLPQLSDVAILDADGQLTYASVKPVPALDNSDRSYFRYHRANDDHTLLITGPIQSRTSGVWVFVVSRRLETTDGKFFGVVVATIESEYFSTFYKTFDLGPGGSISLLHSDGRLLIQWPSLQTGRDmANmVLFQKALPRSPDGYYLTVSPFDGLTKYLAYRRVSRYPLVVTVARTEDSVLSG 285
                                    52   |    62        72        82  |     92       102       112       122       132       142       152       162       172       182       192       202       212       222       232|      242       252       262       272       282   
                                        56-MSE                       85-MSE                                                                                                                                          230-MSE                                                   
                                                                                                                                                                                                                        233-MSE

Chain B from PDB  Type:PROTEIN  Length:241
 aligned with Q6N3S7_RHOPA | Q6N3S7 from UniProtKB/TrEMBL  Length:644

    Alignment length:241
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285 
         Q6N3S7_RHOPA    46 KIALAQSETEMRNLSHSLAEHATHTFQGADVVLDDIVSFMKWRPHPSPVFNERLRALADNLPQLSDVAILDADGQLTYASVKPVPALDNSDRSYFRYHRANDDHTLLITGPIQSRTSGVWVFVVSRRLETTDGKFFGVVVATIESEYFSTFYKTFDLGPGGSISLLHSDGRLLIQWPSLQTGRDMANMVLFQKALPRSPDGYYLTVSPFDGLTKYLAYRRVSRYPLVVTVARTEDSVLSGW 286
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..eeeeeee.....eeee............hhhhhhhhh......eeeeeee......eeeeeeeeee.....eeeeeeeeehhhhhhhhhhh.......eeeeee....eeeee...ee......hhhhhhhhhhh.eeeeeee......eeeeeeee.....eeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lif B  46 KIALAQSETEmRNLSHSLAEHATHTFQGADVVLDDIVSFmKWRPHPSPVFNERLRALADNLPQLSDVAILDADGQLTYASVKPVPALDNSDRSYFRYHRANDDHTLLITGPIQSRTSGVWVFVVSRRLETTDGKFFGVVVATIESEYFSTFYKTFDLGPGGSISLLHSDGRLLIQWPSLQTGRDmANmVLFQKALPRSPDGYYLTVSPFDGLTKYLAYRRVSRYPLVVTVARTEDSVLSGW 286
                                    55|       65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225    |  235       245       255       265       275       285 
                                     56-MSE                       85-MSE                                                                                                                                          230-MSE                                                    
                                                                                                                                                                                                                     233-MSE

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 3LIF)

(no "CATH Domain" information available for 3LIF)

(no "Pfam Domain" information available for 3LIF)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q6N3S7_RHOPA | Q6N3S7)

molecular function
	GO:0000155	phosphorelay sensor kinase activity	Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response.
biological process
	GO:0000160	phosphorelay signal transduction system	A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
	GO:0023014	signal transduction by protein phosphorylation	A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
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: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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		CIT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MPD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asp A:245 - Gly A:246	[ RasMol ]
		Gly A:155 - Pro A:156	[ RasMol ]
		Gly B:155 - Pro B:156	[ RasMol ]
		Leu A:283 - Ser A:284	[ RasMol ]
		Lys A:127 - Pro A:128	[ RasMol ]
		Ser A:284 - Gly A:285	[ RasMol ]
		Ser B:281 - Val B:282	[ RasMol ]
		Trp A:221 - Pro A:222	[ RasMol ]
		Trp B:221 - Pro B:222	[ RasMol ]
		Val A:282 - Leu A:283	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
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	3lif
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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