4A5N - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   REDOXREGULATOR HYPR IN ITS REDUCED 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 :   1.81

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

Keywords :   Transcription, Activator, Dna Binding, Marr-Like (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
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDGHYPRC14S
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Strain	:	TRPC2
	Synonym	:	REDOX REGULATOR HYPR

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	BME	4	Ligand/Ion	BETA-MERCAPTOETHANOL
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	BME	2	Ligand/Ion	BETA-MERCAPTOETHANOL
2	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	BME	2	Ligand/Ion	BETA-MERCAPTOETHANOL
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:41 , ASN A:43 , ARG A:47 , HOH A:2029 , BME B:1118 , HOH B:2058	BINDING SITE FOR RESIDUE BME A1117
2	AC2	SOFTWARE	ARG A:41 , BME A:1117 , ARG B:41 , ASN B:43 , ARG B:47 , HOH B:2022	BINDING SITE FOR RESIDUE BME B1118
3	AC3	SOFTWARE	ARG C:41 , ASN C:43 , ARG C:47 , HOH C:2020 , ARG D:41 , BME D:1115 , HOH D:2048	BINDING SITE FOR RESIDUE BME C1115
4	AC4	SOFTWARE	BME C:1115 , ARG D:41 , ASN D:43 , ARG D:47	BINDING SITE FOR RESIDUE BME D1115
5	AC5	SOFTWARE	PRO A:95 , HOH B:2072 , LYS D:39 , ARG D:91 , HOH D:2012 , HOH D:2072	BINDING SITE FOR RESIDUE EDO D1116

(no "SS Bond" information available for 4A5N)

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

(no "SAP(SNP)/Variant" information available for 4A5N)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_HXLR	PS51118	HxlR-type HTH domain profile.	YYBR_BACSU	14-112	4	A:15-112 B:15-112 C:15-112 D:15-112

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:15-112 B:15-112 - -

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:15-112 D:15-112

(no "Exon" information available for 4A5N)

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:104
 aligned with YYBR_BACSU | P37486 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:104
                                    22        32        42        52        62        72        82        92       102       112    
           YYBR_BACSU    13 GCPVEFTLDVIGGKWKGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGESNRDVLESYRS 116
               SCOP domains d4a5na_ A: automated matches                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh..hhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhhhh..eeeeee.....eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -HTH_HXLR  PDB: A:15-112 UniProt: 14-112                                                            ---- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 4a5n A  13 GSPVEFTLDVIGGKWKGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGESNRDVLESYRS 116
                                    22        32        42        52        62        72        82        92       102       112

Chain B from PDB  Type:PROTEIN  Length:105
 aligned with YYBR_BACSU | P37486 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:105
                                    22        32        42        52        62        72        82        92       102       112     
           YYBR_BACSU    13 GCPVEFTLDVIGGKWKGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGESNRDVLESYRSN 117
               SCOP domains d4a5nb_ B: automated matches                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh..hhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhhhh..eeeeee.....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -HTH_HXLR  PDB: B:15-112 UniProt: 14-112                                                            ----- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 4a5n B  13 GSPVEFTLDVIGGKWKGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGESNRDVLESYRSN 117
                                    22        32        42        52        62        72        82        92       102       112

Chain C from PDB  Type:PROTEIN  Length:101
 aligned with YYBR_BACSU | P37486 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:101
                                    23        33        43        53        63        73        83        93       103       113 
           YYBR_BACSU    14 CPVEFTLDVIGGKWKGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGESNRDVLESY 114
               SCOP domains d4a5nc_ C: automated matches                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh..hhhhhhhhhh...eehhhhhhhh...hhhhhhhhhhhhhhh..eeeeee.....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE HTH_HXLR  PDB: C:15-112 UniProt: 14-112                                                            -- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 4a5n C  14 SPVEFTLDVIGGKWKGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGESNRDVLESY 114
                                    23        33        43        53        63        73        83        93       103       113

Chain D from PDB  Type:PROTEIN  Length:101
 aligned with YYBR_BACSU | P37486 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:101
                                    23        33        43        53        63        73        83        93       103       113 
           YYBR_BACSU    14 CPVEFTLDVIGGKWKGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGESNRDVLESY 114
               SCOP domains d4a5nd_ D: automated matches                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh...hhhhhhhhhh...eehhhhhhhh...hhhhhhhhhhhhhhh..eeeee.......eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE HTH_HXLR  PDB: D:15-112 UniProt: 14-112                                                            -- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 4a5n D  14 SPVEFTLDVIGGKWKGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGESNRDVLESY 114
                                    23        33        43        53        63        73        83        93       103       113

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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( (-)

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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	d4a5na_	A:
1b	d4a5nb_	B:
1c	d4a5nc_	C:
1d	d4a5nd_	D:

(no "CATH Domain" information available for 4A5N)

(no "Pfam Domain" information available for 4A5N)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (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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	Cis Peptide Bonds
		Val A:78 - Pro A:79	[ RasMol ]
		Val B:78 - Pro B:79	[ RasMol ]
		Val C:78 - Pro C:79	[ RasMol ]
		Val D:78 - Pro D:79	[ RasMol ]

Biological Units
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		Biological Unit 2	[ Jena3D ]

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	4a5n
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	YYBR_BACSU \| P37486	:	4a5m

4a5m	REDOX REGULATOR HYPR IN ITS OXIDIZED FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File