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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE PUTATIVE HISTIDINE KINASE VPHK1S-Z8

Authors :   Z. Zhang, W. A. Hendrickson

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

Method :   X-RAY DIFFRACTION

Resolution :   2.59

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 SENSORY BOX/GGDEF FAMILY PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B+
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	EXTRACELLULAR DOMAIN (UNP RESIDUES 28-313)
	Gene	:	VP0354
	Organism Scientific	:	VIBRIO PARAHAEMOLYTICUS
	Organism Taxid	:	670

		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 (1, 2)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

(no "Site" information available for 3LIE)

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

Asymmetric Unit

No.	Residues
1	Leu A:32	-	Leu A:33
2	Tyr B:171	-	Pro B:172
3	Pro B:172	-	Leu B:173

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

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

(no "Exon" information available for 3LIE)

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:266
 aligned with Q87SR8_VIBPA | Q87SR8 from UniProtKB/TrEMBL  Length:626

    Alignment length:273
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299   
         Q87SR8_VIBPA    30 QALLANNVENTAKEALHQLAYTGREYNNIQDQIETISDLLGHSQSLYDYLREPSKANLTILENMWSSVARNQKLYKQIRFLDTSGTEKVRIKYDFKTSIAGPSLILRDKSAREYFKYAQSLDNEQISAWGIELERDKGELVYPLSPSLRILMPISVNDVRQGYLVLNVDIEYLSSLLNYSPVRDFHIELVKHKGFYIASPDESRLYGDIIPERSQFNFSNMYPDIWPRVVSEQAGYSYSGEHLIAFSSIKFVSNEPLHLIIDLSNEQLSKRAT 302
               SCOP domains d3liea1 A:30-206 GGDEF family protein VP0354                                                                                                                                     d3liea2 A:207-302 GGDEF family protein VP0354                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.eeeeeeee....eeeeeee......eee.........hhhhhhhhh......eeeeeee...-------..eeeeeeeeee....eeeeeeeeeehhhhhhhhhee....ee.eeee....eee..hhhhh....hhhhh..hhhhhh..hhhhhhhh.eeeee...eeeeeeeee.....eeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lie A  30 QALLANNVENTAKEALHQLAYTGREYNNIQDQIETISDLLGHSQSLYDYLREPSKANLTILENMWSSVARNQKLYKQIRFLDTSGTEKVRIKYDFKTSIAGPSLILRDKSAREYFKYAQSLDNEQISAWGIELERD-------LSPSLRILMPISVNDVRQGYLVLNVDIEYLSSLLNYSPVRDFHIELVKHKGFYIASPDESRLYGDIIPERSQFNFSNMYPDIWPRVVSEQAGYSYSGEHLIAFSSIKFVSNEPLHLIIDLSNEQLSKRAT 302
                                    39        49        59        69        79        89        99       109       119       129       139       149       159     |   -   |   179       189       199       209       219       229       239       249       259       269       279       289       299   
                                                                                                                                                                 165     173

Chain B from PDB  Type:PROTEIN  Length:262
 aligned with Q87SR8_VIBPA | Q87SR8 from UniProtKB/TrEMBL  Length:626

    Alignment length:268
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292        
         Q87SR8_VIBPA    33 LANNVENTAKEALHQLAYTGREYNNIQDQIETISDLLGHSQSLYDYLREPSKANLTILENMWSSVARNQKLYKQIRFLDTSGTEKVRIKYDFKTSIAGPSLILRDKSAREYFKYAQSLDNEQISAWGIELERDKGELVYPLSPSLRILMPISVNDVRQGYLVLNVDIEYLSSLLNYSPVRDFHIELVKHKGFYIASPDESRLYGDIIPERSQFNFSNMYPDIWPRVVSEQAGYSYSGEHLIAFSSIKFVSNEPLHLIIDLSNEQLSKR 300
               SCOP domains d3lieb1 B:33-206 GGDEF family protein VP0354                                                                                                                                  d3lieb2 B:207-300 GGDEF family protein VP0354                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.eeeeeeee....eeeeeee......eee.........hhhhhhhhh......eeeeeee.------.....eeeeeeeeee....eeeeeeeeeehhhhhhhhhee....ee.eeee....eee..hhhhh....hhhhh..hhhhhh..hhhhhhhh.eeeee...eeeeeeeee.....eeeeeeeeehhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lie B  33 LANNVENTAKEALHQLAYTGREYNNIQDQIETISDLLGHSQSLYDYLREPSKANLTILENMWSSVARNQKLYKQIRFLDTSGTEKVRIKYDFKTSIAGPSLILRDKSAREYFKYAQSLDNEQISAWGIELE------VYPLSPSLRILMPISVNDVRQGYLVLNVDIEYLSSLLNYSPVRDFHIELVKHKGFYIASPDESRLYGDIIPERSQFNFSNMYPDIWPRVVSEQAGYSYSGEHLIAFSSIKFVSNEPLHLIIDLSNEQLSKR 300
                                    42        52        62        72        82        92       102       112       122       132       142       152       162|      172       182       192       202       212       222       232       242       252       262       272       282       292        
                                                                                                                                                            163    170

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Profilin-like (304)

Superfamily: Sensory domain-like (15)

Family: YkuI C-terminal domain-like (5)

Protein domain: GGDEF family protein VP0354 (3)

Vibrio parahaemolyticus [TaxId: 670] (3)

1a	d3liea1	A:30-206
1b	d3lieb1	B:33-206
1c	d3lieb2	B:207-300
1d	d3liea2	A:207-302

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q87SR8_VIBPA | Q87SR8)

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: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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 3lie)

	Cis Peptide Bonds
		Leu A:32 - Leu A:33	[ RasMol ]
		Pro B:172 - Leu B:173	[ RasMol ]
		Tyr B:171 - Pro B:172	[ RasMol ]

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

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	3lie
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
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	Q87SR8_VIBPA \| Q87SR8
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		Disease Information	:	OMIM

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		Age Related Information	:	GenAge

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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UniProtKB/TrEMBL
	Q87SR8_VIBPA \| Q87SR8	:	2p7j 3lid

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 4)

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Pfam Domains (0, 0)

Gene Ontology (4, 4)

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