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Description

Title :   STRUCTURE OF THE CHEYN59D/E89R MOLYBDATE COMPLEX

Authors :   R. M. Immormino, C. A. Starbird, R. E. Silversmith, R. B. Bourret

Date :   06 May 11 (Deposition) - 09 May 12 (Release) - 21 Sep 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Two-Component, Signal Transduction, Response Regulator, Chey, Beta- Alpha Protein, Chemotaxis, Chez, Chex, Chea, Phosphorylation, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. M. Immormino, C. A. Starbird, R. E. Silversmith, R. B. Bourret
Probing Mechanistic Similarities Between Response Regulator Signaling Proteins And Haloacid Dehalogenase Phosphatases.
Biochemistry V. 54 3514 2015
PubMed-ID: 25928369 | Reference-DOI: 10.1021/ACS.BIOCHEM.5B00286

Compounds

Molecule 1 - CHEMOTAXIS PROTEIN CHEY
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28ACHEYN59DE89R
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	B1882, CHEY, JW1871
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12

Structural Features

Chains, Units

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (4, 20)

Asymmetric Unit (4, 20)

No.	Name	Count	Type	Full Name
1	GOL	5	Ligand/Ion	GLYCEROL
2	MN	2	Ligand/Ion	MANGANESE (II) ION
3	MOO	2	Ligand/Ion	MOLYBDATE ION
4	SO4	11	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	MOO	1	Ligand/Ion	MOLYBDATE ION
4	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 10)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	MOO	1	Ligand/Ion	MOLYBDATE ION
4	SO4	7	Ligand/Ion	SULFATE ION

Sites (22, 22)

Asymmetric Unit (22, 22)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:13 , ASP A:57 , ASP A:59 , MOO A:131 , HOH A:145 , HOH A:152	BINDING SITE FOR RESIDUE MN A 130
02	AC2	SOFTWARE	ASP A:57 , TRP A:58 , ASP A:59 , THR A:87 , ALA A:88 , LYS A:109 , MN A:130 , HOH A:210	BINDING SITE FOR RESIDUE MOO A 131
03	AC3	SOFTWARE	MET A:17 , ALA A:88 , LYS A:109 , HOH A:145 , HOH A:162 , HOH A:278	BINDING SITE FOR RESIDUE SO4 A 132
04	AC4	SOFTWARE	GLY A:49 , GLY A:50	BINDING SITE FOR RESIDUE SO4 A 133
05	AC5	SOFTWARE	ASP A:13 , PHE A:14 , SER A:15 , HOH A:195 , HOH A:207 , HOH A:228 , HOH A:236	BINDING SITE FOR RESIDUE SO4 A 134
06	AC6	SOFTWARE	ALA A:2 , LYS A:4 , LEU A:28 , GLY A:29	BINDING SITE FOR RESIDUE SO4 A 135
07	AC7	SOFTWARE	ARG A:19 , LYS A:70 , HOH A:147 , LYS B:126 , HOH B:230	BINDING SITE FOR RESIDUE GOL A 136
08	AC8	SOFTWARE	LYS A:7 , ASN A:32 , GLY A:49 , GLY A:50 , HOH A:181	BINDING SITE FOR RESIDUE GOL A 137
09	AC9	SOFTWARE	LYS A:92 , GLU A:93	BINDING SITE FOR RESIDUE GOL A 138
10	BC1	SOFTWARE	ASP B:13 , ASP B:57 , ASP B:59 , MOO B:131 , HOH B:150 , HOH B:160	BINDING SITE FOR RESIDUE MN B 130
11	BC2	SOFTWARE	ASP B:57 , TRP B:58 , ASP B:59 , THR B:87 , ALA B:88 , LYS B:109 , MN B:130 , HOH B:160 , HOH B:263	BINDING SITE FOR RESIDUE MOO B 131
12	BC3	SOFTWARE	MET B:17 , ALA B:88 , LYS B:109 , HOH B:256 , HOH B:276	BINDING SITE FOR RESIDUE SO4 B 132
13	BC4	SOFTWARE	ASP B:13 , PHE B:14 , SER B:15 , HOH B:155 , HOH B:240 , HOH B:259	BINDING SITE FOR RESIDUE SO4 B 133
14	BC5	SOFTWARE	ARG B:89 , HOH B:191	BINDING SITE FOR RESIDUE SO4 B 134
15	BC6	SOFTWARE	LYS B:4 , LEU B:28 , GLY B:29 , PHE B:30 , HOH B:186	BINDING SITE FOR RESIDUE SO4 B 135
16	BC7	SOFTWARE	HIS B:0 , GLY B:50 , GOL B:140	BINDING SITE FOR RESIDUE SO4 B 136
17	BC8	SOFTWARE	LYS A:92 , LYS B:92 , HOH B:224	BINDING SITE FOR RESIDUE SO4 B 137
18	BC9	SOFTWARE	ARG B:19 , HOH B:142 , HOH B:143 , HOH B:145 , HOH B:210	BINDING SITE FOR RESIDUE SO4 B 138
19	CC1	SOFTWARE	LYS B:7 , ASN B:32 , GLY B:50	BINDING SITE FOR RESIDUE GOL B 139
20	CC2	SOFTWARE	LEU B:46 , GLY B:49 , GLY B:50 , TYR B:51 , ALA B:77 , SO4 B:136 , HOH B:223	BINDING SITE FOR RESIDUE GOL B 140
21	DC1	AUTHOR	ASP A:13 , ASP A:57 , ASP A:59 , MOO A:131 , HOH A:145 , HOH A:152	ACTIVE SITE FOR RESIDUE MN A 130
22	DC2	AUTHOR	ASP B:13 , ASP B:57 , ASP B:59 , MOO B:131 , HOH B:150 , HOH B:160	ACTIVE SITE FOR RESIDUE MN B 130

SS Bonds (0, 0)

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

Cis Peptide Bonds (2, 2)

Asymmetric Unit

No.	Residues
1	Lys A:109	-	Pro A:110
2	Lys B:109	-	Pro B:110

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (1, 2)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RESPONSE_REGULATORY	PS50110	Response regulatory domain profile.	CHEY_ECOLI	7-124	2	A:7-124 B:7-124

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RESPONSE_REGULATORY	PS50110	Response regulatory domain profile.	CHEY_ECOLI	7-124	1	A:7-124 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RESPONSE_REGULATORY	PS50110	Response regulatory domain profile.	CHEY_ECOLI	7-124	1	- B:7-124

Exons (0, 0)

(no "Exon" information available for 3RVR)

Sequences/Alignments

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:130
 aligned with CHEY_ECOLI | P0AE67 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:130
                             1                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129
           CHEY_ECOLI     - -MADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEKLGM 129
               SCOP domains d3rvra_ A: automated matches                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee..hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhh...eeee.......hhhhhhhhhhhh.......eeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------RESPONSE_REGULATORY  PDB: A:7-124 UniProt: 7-124                                                                      ----- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rvr A   0 HMADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWDMPNMDGLELLKTIRADGAMSALPVLMVTARAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEKLGM 129
                                     9        19        29        39        49        59        69        79        89        99       109       119       129

Chain B from PDB  Type:PROTEIN  Length:131
 aligned with CHEY_ECOLI | P0AE67 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:131
                              1                                                                                                                                
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128 
           CHEY_ECOLI     - --MADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEKLGM 129
               SCOP domains d3rvrb_ B: automated matches                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee..hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhh....eeee.......hhhhhhhhhhhh.......eeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------RESPONSE_REGULATORY  PDB: B:7-124 UniProt: 7-124                                                                      ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rvr B  -1 SHMADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWDMPNMDGLELLKTIRADGAMSALPVLMVTARAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEKLGM 129
                                     8        18        28        38        48        58        68        78        88        98       108       118       128

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, 2)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Flavodoxin-like (1057)

Superfamily: CheY-like (258)

Family: CheY-related (166)

Protein domain: automated matches (29)

Escherichia coli K-12 [TaxId: 83333] (17)

1a	d3rvra_	A:
1b	d3rvrb_	B:

CATH Domains (0, 0)

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

Pfam Domains (0, 0)

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

Gene Ontology (12, 12)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CHEY_ECOLI | P0AE67)

molecular function
	GO:0016407	acetyltransferase activity	Catalysis of the transfer of an acetyl group to an acceptor molecule.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0097588	archaeal or bacterial-type flagellum-dependent cell motility	Cell motility due to movement of bacterial- or archaeal-type flagella.
	GO:0071973	bacterial-type flagellum-dependent cell motility	Cell motility due to the motion of one or more bacterial-type flagella. A bacterial-type flagellum is a motor complex composed of an extracellular helical protein filament coupled to a rotary motor embedded in the cell envelope.
	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:0018393	internal peptidyl-lysine acetylation	The addition of an acetyl group to a non-terminal lysine residue in a protein.
	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:0006473	protein acetylation	The addition of an acetyl group to a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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	3rvr
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	CHEY_ECOLI \| P0AE67	:	1a0o 1ab5 1ab6 1bdj 1c4w 1cey 1chn 1cye 1d4z 1djm 1e6k 1e6l 1e6m 1eay 1ehc 1f4v 1ffg 1ffs 1ffw 1fqw 1hey 1jbe 1kmi 1mih 1u8t 1udr 1vlz 1ymu 1ymv 1zdm 2b1j 2id7 2id9 2idm 2lp4 3chy 3f7n 3fft 3ffw 3ffx 3fgz 3myy 3olv 3olw 3olx 3oly 3oo0 3oo1 3rvj 3rvk 3rvl 3rvm 3rvn 3rvo 3rvp 3rvq 3rvs 5chy 5d2c 5dgc 5dkf 6chy

Related Entries Specified in the PDB File

1fqw	STRUCTURE OF ACTIVATED CHEY
3rvj	STRUCTURE OF THE CHEY-BEF3 COMPLEX WITH SUBSTITUTIONS AT 59 AND 89
3rvk	STRUCTURE OF THE CHEY-MN2+ COMPLEX WITH SUBSTITUTIONS AT 59 AND 89
3rvl	STRUCTURE OF THE CHEY-BEF3 COMPLEX WITH SUBSTITUTIONS AT 59 AND 89
3rvm	STRUCTURE OF THE CHEY-MN2+ COMPLEX WITH SUBSTITUTIONS AT 59 AND 89
3rvn	STRUCTURE OF THE CHEY-BEF3 COMPLEX WITH SUBSTITUTIONS AT 59 AND 89
3rvo	STRUCTURE OF THE CHEY-MN2+ COMPLEX WITH SUBSTITUTIONS AT 59 AND 89
3rvp	STRUCTURE OF THE CHEY-BEF3 COMPLEX WITH SUBSTITUTIONS AT 59 AND 89
3rvq	STRUCTURE OF THE CHEY-MN2+ COMPLEX WITH SUBSTITUTIONS AT 59 AND 89
3rvs	TRUCTURE OF THE CHEY N59D/E89R TUNGSTATE COMPLEX