3EEE - JenaLib

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Title :   PROBING THE FUNCTION OF HEME DISTORTION IN THE H-NOX FAMILY

Authors :   C. Olea Jr, E. M. Boon, P. Pellicena, J. Kuriyan, M. A. Marletta

Date :   04 Sep 08 (Deposition) - 25 Nov 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.12

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

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

Reference :   C. Olea, E. M. Boon, P. Pellicena, J. Kuriyan, M. A. Marletta
Probing The Function Of Heme Distortion In The H-Nox Family.
Acs Chem. Biol. V. 3 703 2008
PubMed-ID: 19032091 | Reference-DOI: 10.1021/CB800185H
(for further references see the PDB file header)

Molecule 1 - METHYL-ACCEPTING CHEMOTAXIS PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET20B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	H-NOX DOMAIN, RESIDUES 1-188
	Gene	:	TAR4
	Mutation	:	YES
	Organism Scientific	:	THERMOANAEROBACTER TENGCONGENSIS
	Organism Taxid	:	119072

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 13)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	OXY	4	Ligand/Ion	OXYGEN MOLECULE
4	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	OXY	1	Ligand/Ion	OXYGEN MOLECULE
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	OXY	1	Ligand/Ion	OXYGEN MOLECULE
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	OXY	1	Ligand/Ion	OXYGEN MOLECULE
4	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 4 (3, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	OXY	1	Ligand/Ion	OXYGEN MOLECULE
4	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	MET A:1 , LYS A:2 , PHE A:94 , MET A:98 , HIS A:102 , LEU A:105 , ALA A:115 , LEU A:117 , TYR A:131 , SER A:133 , ARG A:135 , MET A:137 , LEU A:144 , OXY A:493 , HOH A:508 , HOH A:509 , HOH A:548 , HOH A:555	BINDING SITE FOR RESIDUE HEM A 200
02	AC2	SOFTWARE	ILE A:5 , TYR A:140 , LEU A:144 , HEM A:200	BINDING SITE FOR RESIDUE OXY A 493
03	AC3	SOFTWARE	ASP A:45 , VAL A:48 , TRP A:67	BINDING SITE FOR RESIDUE SO4 A 494
04	AC4	SOFTWARE	MET B:1 , LYS B:2 , PHE B:78 , PHE B:86 , PHE B:94 , MET B:98 , HIS B:102 , LEU B:105 , THR B:106 , ALA B:115 , LEU B:117 , TYR B:131 , SER B:133 , ARG B:135 , LEU B:144 , ILE B:145 , OXY B:494 , HOH B:510 , HOH B:518 , HOH B:547 , HOH B:549	BINDING SITE FOR RESIDUE HEM B 200
05	AC5	SOFTWARE	TYR B:140 , HEM B:200	BINDING SITE FOR RESIDUE OXY B 494
06	AC6	SOFTWARE	GLY B:164	BINDING SITE FOR RESIDUE CL B 495
07	AC7	SOFTWARE	MET B:1 , ASP B:45 , VAL B:48 , TRP B:67 , MET B:137 , HOH B:538	BINDING SITE FOR RESIDUE SO4 B 496
08	AC8	SOFTWARE	LYS C:2 , TYR C:85 , PHE C:94 , MET C:98 , HIS C:102 , LEU C:105 , THR C:106 , ALA C:115 , TYR C:131 , SER C:133 , ARG C:135 , LEU C:144 , ILE C:145 , OXY C:495	BINDING SITE FOR RESIDUE HEM C 200
09	AC9	SOFTWARE	ILE C:5 , PHE C:78 , TYR C:140 , HEM C:200	BINDING SITE FOR RESIDUE OXY C 495
10	BC1	SOFTWARE	GLY A:164	BINDING SITE FOR RESIDUE CL C 496
11	BC2	SOFTWARE	MET D:1 , LYS D:2 , PHE D:78 , PHE D:82 , TYR D:85 , PHE D:94 , MET D:98 , HIS D:102 , LEU D:105 , ALA D:115 , LEU D:117 , MET D:129 , TYR D:131 , SER D:133 , ARG D:135 , MET D:137 , LEU D:144 , OXY D:496 , HOH D:508 , HOH D:511	BINDING SITE FOR RESIDUE HEM D 200
12	BC3	SOFTWARE	PHE D:78 , TYR D:140 , LEU D:144 , HEM D:200	BINDING SITE FOR RESIDUE OXY D 496
13	BC4	SOFTWARE	MET D:1 , ASP D:45 , ARG D:49 , HOH D:514	BINDING SITE FOR RESIDUE SO4 D 497

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

(no "Cis Peptide Bond" information available for 3EEE)

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

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

(no "Exon" information available for 3EEE)

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:188
 aligned with Q8RBX6_CALS4 | Q8RBX6 from UniProtKB/TrEMBL  Length:602

    Alignment length:188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        
         Q8RBX6_CALS4     1 MKGTIVGTWIKTLRDLYGNDVVDESLKSVGWEPDRVITPLEDIDDDEVRRIFAKVSEKTGKNVNEIWREVGRQNIKTFSEWFPSYFAGRRLVNFLMMMDEVHLQLTKMIKGATPPRLIAKPVAKDAIEMEYVSKRKMYDYFLGLIEGSSKFFKEEISVEEVERGEKDGFSRLKVRIKFKNPVFEYKKN 188
               SCOP domains d3eeea_ A: Methyl-accepting chemotaxis protein                                                                                                                                               SCOP domains
               CATH domains 3eeeA00 A:1-188 H-NOX domain                                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.........eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhh..eeeeeeeeeee..eeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eee A   1 MKGTIVGTWIKTLRDLYGNDVVDESLKSVGWEPDRVITPLEDIDDDEVRRIFAKVSEKTGKNVNEIWREVGRQNIKTFSEWFPSYFAGRRLVNFLMMMDEVHLQLTKMIKGATPARLIAKPVAKDAIEMEYVSKRKMYDYFLGLIEGSSKFFKEEISVEEVERGEKDGFSRLKVRIKFKNPVFEYKKN 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain B from PDB  Type:PROTEIN  Length:188
 aligned with Q8RBX6_CALS4 | Q8RBX6 from UniProtKB/TrEMBL  Length:602

    Alignment length:188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        
         Q8RBX6_CALS4     1 MKGTIVGTWIKTLRDLYGNDVVDESLKSVGWEPDRVITPLEDIDDDEVRRIFAKVSEKTGKNVNEIWREVGRQNIKTFSEWFPSYFAGRRLVNFLMMMDEVHLQLTKMIKGATPPRLIAKPVAKDAIEMEYVSKRKMYDYFLGLIEGSSKFFKEEISVEEVERGEKDGFSRLKVRIKFKNPVFEYKKN 188
               SCOP domains d3eeeb_ B: Methyl-accepting chemotaxis protein                                                                                                                                               SCOP domains
               CATH domains 3eeeB00 B:1-188 H-NOX domain                                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh........eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhh...eeeeeeeeeee..eeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eee B   1 MKGTIVGTWIKTLRDLYGNDVVDESLKSVGWEPDRVITPLEDIDDDEVRRIFAKVSEKTGKNVNEIWREVGRQNIKTFSEWFPSYFAGRRLVNFLMMMDEVHLQLTKMIKGATPARLIAKPVAKDAIEMEYVSKRKMYDYFLGLIEGSSKFFKEEISVEEVERGEKDGFSRLKVRIKFKNPVFEYKKN 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain C from PDB  Type:PROTEIN  Length:188
 aligned with Q8RBX6_CALS4 | Q8RBX6 from UniProtKB/TrEMBL  Length:602

    Alignment length:188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        
         Q8RBX6_CALS4     1 MKGTIVGTWIKTLRDLYGNDVVDESLKSVGWEPDRVITPLEDIDDDEVRRIFAKVSEKTGKNVNEIWREVGRQNIKTFSEWFPSYFAGRRLVNFLMMMDEVHLQLTKMIKGATPPRLIAKPVAKDAIEMEYVSKRKMYDYFLGLIEGSSKFFKEEISVEEVERGEKDGFSRLKVRIKFKNPVFEYKKN 188
               SCOP domains d3eeec_ C: Methyl-accepting chemotaxis protein                                                                                                                                               SCOP domains
               CATH domains 3eeeC00 C:1-188 H-NOX domain                                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.........eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhh..eeeeeeeeeee..eeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eee C   1 MKGTIVGTWIKTLRDLYGNDVVDESLKSVGWEPDRVITPLEDIDDDEVRRIFAKVSEKTGKNVNEIWREVGRQNIKTFSEWFPSYFAGRRLVNFLMMMDEVHLQLTKMIKGATPARLIAKPVAKDAIEMEYVSKRKMYDYFLGLIEGSSKFFKEEISVEEVERGEKDGFSRLKVRIKFKNPVFEYKKN 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain D from PDB  Type:PROTEIN  Length:188
 aligned with Q8RBX6_CALS4 | Q8RBX6 from UniProtKB/TrEMBL  Length:602

    Alignment length:188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        
         Q8RBX6_CALS4     1 MKGTIVGTWIKTLRDLYGNDVVDESLKSVGWEPDRVITPLEDIDDDEVRRIFAKVSEKTGKNVNEIWREVGRQNIKTFSEWFPSYFAGRRLVNFLMMMDEVHLQLTKMIKGATPPRLIAKPVAKDAIEMEYVSKRKMYDYFLGLIEGSSKFFKEEISVEEVERGEKDGFSRLKVRIKFKNPVFEYKKN 188
               SCOP domains d3eeed_ D: Methyl-accepting chemotaxis protein                                                                                                                                               SCOP domains
               CATH domains 3eeeD00 D:1-188 H-NOX domain                                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh........eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhh...eeeeeeeeeee..eeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eee D   1 MKGTIVGTWIKTLRDLYGNDVVDESLKSVGWEPDRVITPLEDIDDDEVRRIFAKVSEKTGKNVNEIWREVGRQNIKTFSEWFPSYFAGRRLVNFLMMMDEVHLQLTKMIKGATPARLIAKPVAKDAIEMEYVSKRKMYDYFLGLIEGSSKFFKEEISVEEVERGEKDGFSRLKVRIKFKNPVFEYKKN 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: H-NOX domain (8)

Homologous Superfamily: H-NOX domain (8)

Thermoanaerobacter tengcongensis. Organism_taxid: 119072. (7)

1a	3eeeA00	A:1-188
1b	3eeeB00	B:1-188
1c	3eeeC00	C:1-188
1d	3eeeD00	D:1-188

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q8RBX6_CALS4 | Q8RBX6)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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: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.

Asymmetric Unit
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	Cis Peptide Bonds
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	3eee
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	Q8RBX6_CALS4 \| Q8RBX6
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1u4h	WILD-TYPE H-NOX
1u55	WILD-TYPE H-NOX
1u56	WILD-TYPE H-NOX

Description

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Chains, Units

Ligands, Modified Residues, Ions (4, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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