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Title :   CRYSTAL STRUCTURE OF TRANSCRIPTION REGULATORY PROTEIN SLYA FROM SALMONELLA TYPHIMURIUM IN COMPLEX WITH SALICYLATE LIGANDS

Authors :   I. Le Trong, P. S. Brzovic, F. C. Fang, S. J. Libby, R. E. Stenkamp

Date :   10 Jun 08 (Deposition) - 24 Jun 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Slya, Marr, Salmonella, Wing-Helix, Transcription Regulator, Activator, Dna-Binding, Repressor, Transcription Regulation, Virulence (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. S. Brzovic, I. Le Trong, W. W. Navarre, F. C. Fang, R. E. Stenkamp, S. J. Libby
Crystal Structure Of Transcription Regulatory Protein Slya From Salmonella Typhimurium In Complex With Salicylate Ligands.
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - TRANSCRIPTIONAL REGULATOR SLYA
	Atcc	:	14028S
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET16B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SLYA, STM1444
	Organism Scientific	:	SALMONELLA TYPHIMURIUM
	Organism Taxid	:	602
	Strain	:	SGSG 2262
	Synonym	:	SALMOLYSIN, CYTOLYSIN SLYA

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	SAL	6	Ligand/Ion	2-HYDROXYBENZOIC ACID

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	SAL	6	Ligand/Ion	2-HYDROXYBENZOIC ACID

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	SAL	6	Ligand/Ion	2-HYDROXYBENZOIC ACID

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:8 , ALA A:11 , ARG A:15 , TRP A:17 , ARG A:18 , HIS A:39	BINDING SITE FOR RESIDUE SAL A 301
2	AC2	SOFTWARE	SER B:8 , ALA B:11 , ARG B:15 , ARG B:18 , ILE B:21 , HIS B:39	BINDING SITE FOR RESIDUE SAL B 302
3	AC3	SOFTWARE	ARG A:24 , LYS A:110 , GLU A:114	BINDING SITE FOR RESIDUE SAL A 303
4	AC4	SOFTWARE	ARG B:24 , LYS B:110 , GLU B:114	BINDING SITE FOR RESIDUE SAL B 304
5	AC5	SOFTWARE	THR A:33 , THR A:37 , ILE A:59 , THR A:67	BINDING SITE FOR RESIDUE SAL A 305
6	AC6	SOFTWARE	THR B:33 , THR B:37 , ILE B:59 , THR B:67	BINDING SITE FOR RESIDUE SAL B 306

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

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

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_MARR_2	PS50995	MarR-type HTH domain profile.	SLYA_SALTY	2-135	2	A:3-136 B:3-136
2	HTH_MARR_1	PS01117	MarR-type HTH domain signature.	SLYA_SALTY	62-96	2	A:63-97 B:63-97

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_MARR_2	PS50995	MarR-type HTH domain profile.	SLYA_SALTY	2-135	2	A:3-136 -
2	HTH_MARR_1	PS01117	MarR-type HTH domain signature.	SLYA_SALTY	62-96	2	A:63-97 -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_MARR_2	PS50995	MarR-type HTH domain profile.	SLYA_SALTY	2-135	2	- B:3-136
2	HTH_MARR_1	PS01117	MarR-type HTH domain signature.	SLYA_SALTY	62-96	2	- B:63-97

(no "Exon" information available for 3DEU)

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:132
 aligned with SLYA_SALTY | P40676 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
           SLYA_SALTY     1 MESPLGSDLARLVRIWRALIDHRLKPLELTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQTCASDRRAKRIKLTEKADALIAEMEEVIHKTRGEILAGISSEEIELLIKLIAKLEHNIMEL 140
               SCOP domains d3deua1 A:2-141 Transcriptional regulator SlyA                                                                                               SCOP domains
               CATH domains 3deuA00 A:2-141 'winged helix' repressor DNA binding domain                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...eehhhhhhhhh.hhhhhhhhhhhhhhh..eee.--------.eeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -HTH_MARR_2  PDB: A:3-136 UniProt: 2-135                                                                                               ----- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------HTH_MARR_1  PDB: A:63-97           -------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3deu A   2 LESPLGSDLARLVRIWRALIDHRLKPLELTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQ--------KRIKLTEKAEPLIAEMEEVIHKTRGEILAGISSEEIELLIKLIAKLEHNIMEL 141
                                    11        21        31        41        51        61        71        |-       |91       101       111       121       131       141
                                                                                                         80       89

Chain B from PDB  Type:PROTEIN  Length:130
 aligned with SLYA_SALTY | P40676 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
           SLYA_SALTY     1 MESPLGSDLARLVRIWRALIDHRLKPLELTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQTCASDRRAKRIKLTEKADALIAEMEEVIHKTRGEILAGISSEEIELLIKLIAKLEHNIMEL 140
               SCOP domains d3deub_ B: Transcriptional regulator SlyA                                                                                                    SCOP domains
               CATH domains 3deuB00 B:2-141 'winged helix' repressor DNA binding domain                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhhhhh..ee.----------..ee..hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -HTH_MARR_2  PDB: B:3-136 UniProt: 2-135                                                                                               ----- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------HTH_MARR_1  PDB: B:63-97           -------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3deu B   2 LESPLGSDLARLVRIWRALIDHRLKPLELTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISR----------RIKLTEKAEPLIAEMEEVIHKTRGEILAGISSEEIELLIKLIAKLEHNIMEL 141
                                    11        21        31        41        51        61        71       | -        91       101       111       121       131       141
                                                                                                        79         90

Legend:		→ Mismatch	(orange background)
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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(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

)

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: Transcriptional regulator SlyA (4)

Salmonella typhimurium [TaxId: 90371] (3)

1a	d3deua1	A:2-141
1b	d3deub_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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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)

Salmonella typhimurium. Organism_taxid: 602. Strain: sgsg 2262. (1)

1a	3deuB00	B:2-141
1b	3deuA00	A:2-141

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (SLYA_SALTY | P40676)

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:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	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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