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Title :   THE STRUCTURE OF A PUTATIVE MARR FAMILY TRANSCRIPTIONAL REGULATOR FROM CLOSTRIDIUM ACETOBUTYLICUM

Authors :   M. E. Cuff, L. Bigelow, S. Moy, A. Joachimiak, Midwest Center For Str Genomics (Mcsg)

Date :   17 Sep 09 (Deposition) - 22 Dec 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Marr, Emrr, Transcriptional Regulator, Dna-Binding Protein, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Dna-Binding, Transcription, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. E. Cuff, L. Bigelow, S. Moy, A. Joachimiak
The Structure Of A Putative Marr Family Transcriptional Regulator From Clostridium Acetobutylicum
To Be Published
PubMed: search

Molecule 1 - TRANSCRIPTIONAL REGULATOR, MARR/EMRR FAMILY
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	MODIFIED BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	CAC2486, CA_C2486
	Organism Scientific	:	CLOSTRIDIUM ACETOBUTYLICUM
	Organism Taxid	:	1488
	Strain	:	ATCC 824

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 20)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	IMD	1	Ligand/Ion	IMIDAZOLE
3	K	1	Ligand/Ion	POTASSIUM ION
4	MSE	16	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	IMD	-1	Ligand/Ion	IMIDAZOLE
3	K	-1	Ligand/Ion	POTASSIUM ION
4	MSE	11	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (3, 14)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	IMD	2	Ligand/Ion	IMIDAZOLE
3	K	-1	Ligand/Ion	POTASSIUM ION
4	MSE	10	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:123 , LYS A:124 , LEU A:126 , GLN A:131 , HOH A:186 , HOH A:214 , SER B:53 , HOH B:195	BINDING SITE FOR RESIDUE K A 146
2	AC2	SOFTWARE	TYR B:48 , GLN B:51 , VAL B:100 , PRO B:102 , ALA B:105	BINDING SITE FOR RESIDUE GOL B 146
3	AC3	SOFTWARE	PRO B:11 , TYR C:83 , HOH C:173	BINDING SITE FOR RESIDUE IMD C 146
4	AC4	SOFTWARE	SER B:73 , ASN C:112	BINDING SITE FOR RESIDUE GOL C 147

(no "SS Bond" information available for 3JW4)

(no "Cis Peptide Bond" information available for 3JW4)

(no "SAP(SNP)/Variant" information available for 3JW4)

(no "PROSITE Motif" information available for 3JW4)

(no "Exon" information available for 3JW4)

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
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Chain A from PDB  Type:PROTEIN  Length:123
 aligned with Q97G83_CLOAB | Q97G83 from UniProtKB/TrEMBL  Length:145

    Alignment length:137
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       
         Q97G83_CLOAB     9 DTPYSYLIRSIGMKLKTSADARLAELGLNSQQGRMIGYIYENQESGIIQKDLAQFFGRRGASITSMLQGLEKKGYIERRIPENNARQKNIYVLPKGAALVEEFNNIFLEVEESITKGLTKDEQKQLMSILIKVNRSM 145
               SCOP domains d3jw4a_ A: automated matches                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhh------hhhhhhhhhhhh......--------.....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jw4 A   9 DTPYSYLIRSIGmKLKTSADARLAELGLNSQQGRmIGYIYENQESGIIQKDLAQF------SITSmLQGLEKKGYIERR--------KNIYVLPKGAALVEEFNNIFLEVEESITKGLTKDEQKQLmSILIKVNRSm 145
                                    18  |     28        38    |   48        58    |    - |   |  78        |-       |98       108       118       128      |138      |
                                       21-MSE                43-MSE              63     70   |           87       96                                    135-MSE   145-MSE
                                                                                            74-MSE

Chain B from PDB  Type:PROTEIN  Length:128
 aligned with Q97G83_CLOAB | Q97G83 from UniProtKB/TrEMBL  Length:145

    Alignment length:139
                                    16        26        36        46        56        66        76        86        96       106       116       126       136         
         Q97G83_CLOAB     7 LMDTPYSYLIRSIGMKLKTSADARLAELGLNSQQGRMIGYIYENQESGIIQKDLAQFFGRRGASITSMLQGLEKKGYIERRIPENNARQKNIYVLPKGAALVEEFNNIFLEVEESITKGLTKDEQKQLMSILIKVNRSM 145
               SCOP domains d3jw4b_ B: automated matches                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhh------.hhhhhhhhhhhh..eeee..-----..eeeehhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jw4 B   7 LmDTPYSYLIRSIGmKLKTSADARLAELGLNSQQGRmIGYIYENQESGIIQKDLAQ------ASITSmLQGLEKKGYIERRIP-----QKNIYVLPKGAALVEEFNNIFLEVEESITKGLTKDEQKQLmSILIKVNRSm 145
                             |      16    |   26        36      | 46        56     |   -  |    |76        86  |     96       106       116       126       136        |
                             |           21-MSE                43-MSE             62     69    |             89    95                                     135-MSE   145-MSE
                             8-MSE                                                            74-MSE

Chain C from PDB  Type:PROTEIN  Length:130
 aligned with Q97G83_CLOAB | Q97G83 from UniProtKB/TrEMBL  Length:145

    Alignment length:137
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       
         Q97G83_CLOAB     9 DTPYSYLIRSIGMKLKTSADARLAELGLNSQQGRMIGYIYENQESGIIQKDLAQFFGRRGASITSMLQGLEKKGYIERRIPENNARQKNIYVLPKGAALVEEFNNIFLEVEESITKGLTKDEQKQLMSILIKVNRSM 145
               SCOP domains d3jw4c_ C: automated matches                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------MarR-3jw4C01 C:36-96                                         ------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------MarR-3jw4C02 C:36-96                                         ------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ---------------------------MarR-3jw4C03 C:36-96                                         ------------------------------------------------- Pfam domains (3)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhh.---hhhhhhhhhhhhh..eeee..----...eeeehhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jw4 C   9 DTPYSYLIRSIGmKLKTSADARLAELGLNSQQGRmIGYIYENQESGIIQKDLAQFFG---ASITSmLQGLEKKGYIERRIP----RQKNIYVLPKGAALVEEFNNIFLEVEESITKGLTKDEQKQLmSILIKVNRSm 145
                                    18  |     28        38    |   48        58      |  -|    |  78        88|    |  98       108       118       128      |138      |
                                       21-MSE                43-MSE                65  69    |             89   94                                      135-MSE   145-MSE
                                                                                            74-MSE

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)

Clostridium acetobutylicum [TaxId: 1488] (1)

1a	d3jw4a_	A:
1b	d3jw4b_	B:
1c	d3jw4c_	C:

(no "CATH Domain" information available for 3JW4)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: MarR (16)

Clostridium acetobutylicum (1)

1a	MarR-3jw4C01	C:36-96
1b	MarR-3jw4C02	C:36-96
1c	MarR-3jw4C03	C:36-96

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (Q97G83_CLOAB | Q97G83)

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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