2A61 - JenaLib

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Title :   THE CRYSTAL STRUCTURE OF TRANSCRIPTIONAL REGULATOR TM0710 FROM THERMOTOGA MARITIMA

Authors :   V. V. Lunin, E. Evdokimova, M. Kudritska, C. Chang, A. Joachimiak, A. Edwards, A. Savchenko, Midwest Center For Structural Genomics (Mcsg)

Date :   01 Jul 05 (Deposition) - 19 Jul 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Tm0710, Apc4350, Mcsg, Midwest Center For Structural Genomics, Psi, Protein Structure Initiative, Transcriptional Regulator, Marr (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. V. Lunin, E. Evdokimova, M. Kudritska, C. Chang, A. Joachimiak, A. Edwards, A. Savchenko
The Crystal Structure Of Transcriptional Regulator Tm0710 From Thermotoga Maritima
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - TRANSCRIPTIONAL REGULATOR TM0710
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	MODIFIED PET15B
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336

		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)

(no "Ligand,Modified Residues,Ions" information available for 2A61)

(no "Site" information available for 2A61)

Asymmetric Unit

No.	Residues
1	A:16	-	B:16
2	C:16	-	D:16

(no "Cis Peptide Bond" information available for 2A61)

(no "SAP(SNP)/Variant" information available for 2A61)

(no "PROSITE Motif" information available for 2A61)

(no "Exon" information available for 2A61)

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:142
 aligned with Q9WZG9_THEMA | Q9WZG9 from UniProtKB/TrEMBL  Length:143

    Alignment length:142
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  
         Q9WZG9_THEMA     2 KQPFERILREICFMVKVEGRKVLRDFGITPAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIEKVIERRENFIEKITSDLGKEKSSKILDYLKELKGVMERNFSKQ 143
               SCOP domains d2a61a1 A:5-143 Transcriptional regulator TM0710                                                                                           --- SCOP domains
               CATH domains 2a61A00 A:5-146 'winged helix' repressor DNA binding domain                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeeee..eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a61 A   5 KQPFERILREICFMVKVEGRKVLRDFGITPAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIEKVIERRENFIEKITSDLGKEKSSKILDYLKELKGVMERNFSKQ 146
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144

Chain B from PDB  Type:PROTEIN  Length:137
 aligned with Q9WZG9_THEMA | Q9WZG9 from UniProtKB/TrEMBL  Length:143

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
         Q9WZG9_THEMA     2 KQPFERILREICFMVKVEGRKVLRDFGITPAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIEKVIERRENFIEKITSDLGKEKSSKILDYLKELKGVMERNFSK 142
               SCOP domains d2a61b_ B: automated matches                                                                                                                  SCOP domains
               CATH domains 2a61B00 B:5-145 'winged helix' repressor DNA binding domain                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeee.----..eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a61 B   5 KQPFERILREICFMVKVEGRKVLRDFGITPAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPD----RAYFLVITRKGEEVIEKVIERRENFIEKITSDLGKEKSSKILDYLKELKGVMERNFSK 145
                                    14        24        34        44        54        64        74        |-   |    94       104       114       124       134       144 
                                                                                                         83   88

Chain C from PDB  Type:PROTEIN  Length:142
 aligned with Q9WZG9_THEMA | Q9WZG9 from UniProtKB/TrEMBL  Length:143

    Alignment length:142
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  
         Q9WZG9_THEMA     2 KQPFERILREICFMVKVEGRKVLRDFGITPAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIEKVIERRENFIEKITSDLGKEKSSKILDYLKELKGVMERNFSKQ 143
               SCOP domains d2a61c_ C: automated matches                                                                                                                   SCOP domains
               CATH domains 2a61C00 C:5-146 'winged helix' repressor DNA binding domain                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeeee..eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a61 C   5 KQPFERILREICFMVKVEGRKVLRDFGITPAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIEKVIERRENFIEKITSDLGKEKSSKILDYLKELKGVMERNFSKQ 146
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144

Chain D from PDB  Type:PROTEIN  Length:137
 aligned with Q9WZG9_THEMA | Q9WZG9 from UniProtKB/TrEMBL  Length:143

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
         Q9WZG9_THEMA     2 KQPFERILREICFMVKVEGRKVLRDFGITPAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIEKVIERRENFIEKITSDLGKEKSSKILDYLKELKGVMERNFSK 142
               SCOP domains d2a61d_ D: automated matches                                                                                                                  SCOP domains
               CATH domains 2a61D00 D:5-145 'winged helix' repressor DNA binding domain                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeee.----..eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a61 D   5 KQPFERILREICFMVKVEGRKVLRDFGITPAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPD----RAYFLVITRKGEEVIEKVIERRENFIEKITSDLGKEKSSKILDYLKELKGVMERNFSK 145
                                    14        24        34        44        54        64        74        |-   |    94       104       114       124       134       144 
                                                                                                         83   88

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(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All alpha proteins (14657)

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

Superfamily: Winged helix DNA-binding domain (576)

Family: MarR-like transcriptional regulators (34)

Protein domain: automated matches (7)

Thermotoga maritima [TaxId: 2336] (1)

1a	d2a61b_	B:
1b	d2a61c_	C:
1c	d2a61d_	D:

Protein domain: Transcriptional regulator TM0710 (1)

Thermotoga maritima [TaxId: 2336] (1)

d2a61a1

A:5-143

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: 'winged helix' repressor DNA binding domain (507)

Thermotoga maritima. Organism_taxid: 2336. (3)

1a	2a61B00	B:5-145
1b	2a61D00	D:5-145
1c	2a61A00	A:5-146
1d	2a61C00	C:5-146

(no "Pfam Domain" information available for 2A61)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q9WZG9_THEMA | Q9WZG9)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
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.

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