4A5M - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   REDOX REGULATOR HYPR IN ITS OXIDIZED FORM

Authors :   G. J. Palm, P. Waack, R. J. Read, W. Hinrichs

Date :   26 Oct 11 (Deposition) - 11 Jan 12 (Release) - 23 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Transcription, Activator, Dna-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. J. Palm, B. K. Chi, P. Waack, K. Gronau, D. Becher, D. Albrecht, W. Hinrichs, R. J. Read, H. Antelmann
Structural Insights Into The Redox-Switch Mechanism Of The Marr/Duf24-Type Regulator Hypr
Nucleic Acids Res. V. 40 4178 2012
PubMed-ID: 22238377 | Reference-DOI: 10.1093/NAR/GKR1316

Molecule 1 - UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL REGULATOR YYBR
	Chains	:	A, B, C, D, E, F, G, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDGHYPR
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Strain	:	TRPC2
	Synonym	:	REDOX REGULATOR HYPR

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:					E	F
Biological Unit 4 (1x)	:							G	H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 10)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	EDO	9	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	4	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 3 (1, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	4	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR D:87 , GLU D:88 , LYS E:39 , TYR E:75 , LYS E:81	BINDING SITE FOR RESIDUE EDO D1111
02	AC2	SOFTWARE	ARG A:62 , ARG E:62 , ARG E:72	BINDING SITE FOR RESIDUE EDO E1110
03	AC3	SOFTWARE	ARG A:62 , ARG E:41	BINDING SITE FOR RESIDUE EDO E1111
04	AC4	SOFTWARE	HIS A:76 , GLN A:77 , VAL A:78 , GLU E:63 , ALA E:66 , ASP E:67	BINDING SITE FOR RESIDUE EDO A1110
05	AC5	SOFTWARE	LYS A:39 , TYR A:75 , LYS A:81 , GLU H:88	BINDING SITE FOR RESIDUE EDO A1111
06	AC6	SOFTWARE	ILE A:36 , LEU C:98	BINDING SITE FOR RESIDUE EDO A1112
07	AC7	SOFTWARE	TYR E:33	BINDING SITE FOR RESIDUE EDO E1112
08	AC8	SOFTWARE	GLN F:99 , LYS G:39	BINDING SITE FOR RESIDUE CL F1111
09	AC9	SOFTWARE	GLU D:65 , VAL D:70 , HIS D:71 , ARG D:72 , HOH D:2002 , TYR E:75 , HIS E:76 , GLN E:77	BINDING SITE FOR RESIDUE EDO E1113
10	BC1	SOFTWARE	ASN A:43 , LYS A:81 , VAL A:82	BINDING SITE FOR RESIDUE EDO A1113

Asymmetric Unit

No.	Residues
1	A:14	-	B:49
2	A:49	-	B:14
3	C:14	-	D:49
4	C:49	-	D:14
5	E:14	-	F:49
6	E:49	-	F:14
7	G:14	-	H:49
8	G:49	-	H:14

Asymmetric Unit

No.	Residues
1	Val A:78	-	Pro A:79
2	Val B:78	-	Pro B:79
3	Val C:78	-	Pro C:79
4	Val D:78	-	Pro D:79
5	Val E:78	-	Pro E:79
6	Val F:78	-	Pro F:79
7	Val G:78	-	Pro G:79
8	Val H:78	-	Pro H:79

(no "SAP(SNP)/Variant" information available for 4A5M)

Asymmetric Unit (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_HXLR	PS51118	HxlR-type HTH domain profile.	YYBR_BACSU	14-112	8	A:14-109 B:14-110 C:14-109 D:14-110 E:14-109 F:14-110 G:14-109 H:14-110

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_HXLR	PS51118	HxlR-type HTH domain profile.	YYBR_BACSU	14-112	2	A:14-109 B:14-110 - - - - - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_HXLR	PS51118	HxlR-type HTH domain profile.	YYBR_BACSU	14-112	2	- - C:14-109 D:14-110 - - - -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_HXLR	PS51118	HxlR-type HTH domain profile.	YYBR_BACSU	14-112	2	- - - - E:14-109 F:14-110 - -

Biological Unit 4 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_HXLR	PS51118	HxlR-type HTH domain profile.	YYBR_BACSU	14-112	2	- - - - - - G:14-109 H:14-110

(no "Exon" information available for 4A5M)

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:96
 aligned with YYBR_BACSU | P37486 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:96
                                    23        33        43        53        63        73        83        93       103      
           YYBR_BACSU    14 CPVEFTLDVIGGKWKGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGESNRD 109
               SCOP domains d4a5ma_ A: automated matches                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhh..hhhhhhhhhh...eehhhhhhhh...hhhhhhhhhhhhhhh..eeeeee.....eeeeee..hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE HTH_HXLR  PDB: A:14-109 UniProt: 14-112                                                          PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 4a5m A  14 CPVEFTLDVIGGKWKGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGESNRD 109
                                    23        33        43        53        63        73        83        93       103

Chain B from PDB  Type:PROTEIN  Length:97
 aligned with YYBR_BACSU | P37486 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:97
                                    23        33        43        53        63        73        83        93       103       
           YYBR_BACSU    14 CPVEFTLDVIGGKWKGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGESNRDV 110
               SCOP domains d4a5mb_ B: automated matches                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh..hhhhhhhhhh...eehhhhhhhh...hhhhhhhhhhhhhhh..eeeeee.....eeeeee..hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE HTH_HXLR  PDB: B:14-110 UniProt: 14-112                                                           PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4a5m B  14 CPVEFTLDVIGGKWKGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGESNRDV 110
                                    23        33        43        53        63        73        83        93       103

Chain C from PDB  Type:PROTEIN  Length:96
 aligned with YYBR_BACSU | P37486 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:96
                                    23        33        43        53        63        73        83        93       103      
           YYBR_BACSU    14 CPVEFTLDVIGGKWKGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGESNRD 109
               SCOP domains d4a5mc_ C: automated matches                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhh..hhhhhhhhhh...eehhhhhhhh...hhhhhhhhhhhhhhh..eeeeee.....eeeeee..hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE HTH_HXLR  PDB: C:14-109 UniProt: 14-112                                                          PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 4a5m C  14 CPVEFTLDVIGGKWKGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGESNRD 109
                                    23        33        43        53        63        73        83        93       103

Chain D from PDB  Type:PROTEIN  Length:97
 aligned with YYBR_BACSU | P37486 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:97
                                    23        33        43        53        63        73        83        93       103       
           YYBR_BACSU    14 CPVEFTLDVIGGKWKGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGESNRDV 110
               SCOP domains d4a5md_ D: automated matches                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh..hhhhhhhhhh...eehhhhhhhh...hhhhhhhhhhhhhhh..eeeeee.....eeeeee..hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE HTH_HXLR  PDB: D:14-110 UniProt: 14-112                                                           PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4a5m D  14 CPVEFTLDVIGGKWKGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGESNRDV 110
                                    23        33        43        53        63        73        83        93       103

Chain E from PDB  Type:PROTEIN  Length:96
 aligned with YYBR_BACSU | P37486 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:96
                                    23        33        43        53        63        73        83        93       103      
           YYBR_BACSU    14 CPVEFTLDVIGGKWKGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGESNRD 109
               SCOP domains d4a5me_ E: automated matches                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhh..hhhhhhhhhh...eehhhhhhhh...hhhhhhhhhhhhhhh..eeeeee.....eeeeee..hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE HTH_HXLR  PDB: E:14-109 UniProt: 14-112                                                          PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 4a5m E  14 CPVEFTLDVIGGKWKGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGESNRD 109
                                    23        33        43        53        63        73        83        93       103

Chain F from PDB  Type:PROTEIN  Length:97
 aligned with YYBR_BACSU | P37486 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:97
                                    23        33        43        53        63        73        83        93       103       
           YYBR_BACSU    14 CPVEFTLDVIGGKWKGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGESNRDV 110
               SCOP domains d4a5mf_ F: automated matches                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh..hhhhhhhhhh...eehhhhhhhh...hhhhhhhhhhhhhhh..eeeeee.....eeeeee..hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE HTH_HXLR  PDB: F:14-110 UniProt: 14-112                                                           PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4a5m F  14 CPVEFTLDVIGGKWKGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGESNRDV 110
                                    23        33        43        53        63        73        83        93       103

Chain G from PDB  Type:PROTEIN  Length:96
 aligned with YYBR_BACSU | P37486 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:96
                                    23        33        43        53        63        73        83        93       103      
           YYBR_BACSU    14 CPVEFTLDVIGGKWKGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGESNRD 109
               SCOP domains d4a5mg_ G: automated matches                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhh..hhhhhhhhhh...eehhhhhhhh...hhhhhhhhhhhhhhh..eeeeee.....eeeeee..hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE HTH_HXLR  PDB: G:14-109 UniProt: 14-112                                                          PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 4a5m G  14 CPVEFTLDVIGGKWKGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGESNRD 109
                                    23        33        43        53        63        73        83        93       103

Chain H from PDB  Type:PROTEIN  Length:97
 aligned with YYBR_BACSU | P37486 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:97
                                    23        33        43        53        63        73        83        93       103       
           YYBR_BACSU    14 CPVEFTLDVIGGKWKGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGESNRDV 110
               SCOP domains d4a5mh_ H: automated matches                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh..hhhhhhhhhh...eehhhhhhhh...hhhhhhhhhhhhhhh..eeeeee.....eeeeee..hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE HTH_HXLR  PDB: H:14-110 UniProt: 14-112                                                           PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4a5m H  14 CPVEFTLDVIGGKWKGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGESNRDV 110
                                    23        33        43        53        63        73        83        93       103

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: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: Winged helix DNA-binding domain (576)

Family: automated matches (118)

Protein domain: automated matches (118)

Bacillus subtilis [TaxId: 1423] (6)

1a	d4a5ma_	A:
1b	d4a5mb_	B:
1c	d4a5mc_	C:
1d	d4a5md_	D:
1e	d4a5me_	E:
1f	d4a5mf_	F:
1g	d4a5mg_	G:
1h	d4a5mh_	H:

(no "CATH Domain" information available for 4A5M)

(no "Pfam Domain" information available for 4A5M)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F,G,H (YYBR_BACSU | P37486)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

Asymmetric Unit
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	4a5m
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	YYBR_BACSU \| P37486	:	4a5n

4a5n	REDOXREGULATOR HYPR IN ITS REDUCED FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 10)

Sites (10, 10)

SS Bonds (8, 8)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 8)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 8)

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Pfam Domains (0, 0)

Gene Ontology (3, 3)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File