1O3T

PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES

Replaces:  1DBC

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0003677	molecular_function	DNA binding
A	0003680	molecular_function	minor groove of adenine-thymine-rich DNA binding
A	0003700	molecular_function	DNA-binding transcription factor activity
A	0005515	molecular_function	protein binding
A	0005829	cellular_component	cytosol
A	0006351	biological_process	DNA-templated transcription
A	0006355	biological_process	regulation of DNA-templated transcription
A	0008301	molecular_function	DNA binding, bending
A	0030552	molecular_function	cAMP binding
A	0032993	cellular_component	protein-DNA complex
A	0042802	molecular_function	identical protein binding
A	0043565	molecular_function	sequence-specific DNA binding
A	0045013	biological_process	carbon catabolite repression of transcription
A	0045892	biological_process	negative regulation of DNA-templated transcription
A	0045893	biological_process	positive regulation of DNA-templated transcription
B	0000166	molecular_function	nucleotide binding
B	0003677	molecular_function	DNA binding
B	0003680	molecular_function	minor groove of adenine-thymine-rich DNA binding
B	0003700	molecular_function	DNA-binding transcription factor activity
B	0005515	molecular_function	protein binding
B	0005829	cellular_component	cytosol
B	0006351	biological_process	DNA-templated transcription
B	0006355	biological_process	regulation of DNA-templated transcription
B	0008301	molecular_function	DNA binding, bending
B	0030552	molecular_function	cAMP binding
B	0032993	cellular_component	protein-DNA complex
B	0042802	molecular_function	identical protein binding
B	0043565	molecular_function	sequence-specific DNA binding
B	0045013	biological_process	carbon catabolite repression of transcription
B	0045892	biological_process	negative regulation of DNA-templated transcription
B	0045893	biological_process	positive regulation of DNA-templated transcription

Functional Information from PDB Data

site_id	AC1
Number of Residues	13
Details	BINDING SITE FOR RESIDUE CMP B 761

Chain	Residue
A	LEU124
B	SER83
B	ALA84
B	ARG123
B	THR127
A	SER128
B	ILE30
B	VAL49
B	SER62
B	GLY71
B	GLU72
B	LEU73
B	ARG82

---

site_id	AC2
Number of Residues	12
Details	BINDING SITE FOR RESIDUE CMP A 762

Chain	Residue
A	VAL49
A	LEU61
A	ILE70
A	GLY71
A	GLU72
A	LEU73
A	ARG82
A	SER83
A	ALA84
A	THR127
B	LEU124
B	SER128

---

Functional Information from PROSITE/UniProt

site_id	PS00042
Number of Residues	24
Details	HTH_CRP_1 Crp-type HTH domain signature. ITRqeIGqIVGcSreTv.GRiLkmL

Chain	Residue	Details
A	ILE167-LEU190

---

site_id	PS00888
Number of Residues	17
Details	CNMP_BINDING_1 Cyclic nucleotide-binding domain signature 1. LIhQGEkAEtLYYIvkG

Chain	Residue	Details
A	LEU29-GLY45

---

site_id	PS00889
Number of Residues	19
Details	CNMP_BINDING_2 Cyclic nucleotide-binding domain signature 2. IGElGLfeegqe.....RSAwVrA

Chain	Residue	Details
A	ILE70-ALA88

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	12
Details	DNA binding: {"description":"H-T-H motif","evidences":[{"source":"PROSITE-ProRule","id":"PRU00387","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	4
Details	Region: {"description":"Activating region 2 (AR2); probably contacts the N-terminus of RpoA","evidences":[{"source":"PubMed","id":"8978616","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	12
Details	Region: {"description":"Activating region 3 (AR3); probably contacts sigma-70 (RpoD)","evidences":[{"source":"PubMed","id":"10860739","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"10860740","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	18
Details	Region: {"description":"Activating region 1 (AR1); probably contacts the C-terminus of RpoA","evidences":[{"source":"PubMed","id":"7966284","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8392187","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	42
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11124031","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12202833","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"1653449","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"2828639","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"6286624","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8757802","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	Site: {"description":"Activating region 2 (AR2); probably contacts the N-terminus of RpoA","evidences":[{"source":"PubMed","id":"8978616","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	2
Details	Site: {"description":"Activating region 2 (AR2); probably contacts the N-terminus of RpoA","evidences":[{"source":"PubMed","id":"15520470","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8978616","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"18723842","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---