Structure of PDB 1smy Chain F

Receptor sequence

>1smyF (length=345) Species: 274 (Thermus thermophilus)

KISTSDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLD
PDLIREVVRAKILGSARVRHIPGLKETLDPKTVEEIDQKLKSLPKEHKRY
LHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRA
VEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSR
TARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGD
EKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRK
GLIDGEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKLRDFLD

3D structure

• PDB: 1smy Structural basis for transcription regulation by alarmone ppGpp
• Chain: F
• Resolution: 2.7 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	MG	F	K409 S413 R416	K331 S335 R338
BS02	MG	F	R372 K373 G378	R299 K300 G305
BS03	MG	F	R142 G146	R69 G73
BS04	MG	F	P80 Y84	P7 Y11
BS05	MG	F	E181 R184	E108 R111
BS06	MG	F	P286 T287 I291	P213 T214 I218
BS07	MG	F	L349 L422	L276 L344
BS08	MG	F	T203 G204	T130 G131
BS09	MG	F	T307 L308	T234 L235
BS10	MG	F	V386 G387 F389	V308 G309 F311
BS11	MG	F	S362 I400	S289 I322
BS12	MG	F	E324 K325	E251 K252
BS13	MG	F	G391 V392	G313 V314
BS14	MG	F	K230 R231	K157 R158

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003700 DNA-binding transcription factor activity
• GO:0016987 sigma factor activity

Biological Process

• GO:0006352 DNA-templated transcription initiation
• GO:0006355 regulation of DNA-templated transcription
• GO:0010468 regulation of gene expression
• GO:2000142 regulation of DNA-templated transcription initiation

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:1smy, PDBe:1smy, PDBj:1smy
• PDBsum: 1smy
• PubMed: 15109491
• UniProt: Q72L95|SIGA_THET2 RNA polymerase sigma factor SigA (Gene Name=sigA)