1RZR

crystal structure of transcriptional regulator-phosphoprotein-DNA complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
E [auth G]	d1rzrg1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	GalR/LacI-like bacterial regulator	Glucose-resistance amylase regulator CcpA, N-terminal domain	(Priestia megaterium ) [TaxId: 1404 ],	SCOPe (2.08)
E [auth G]	d1rzrg2	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	L-arabinose binding protein-like	Glucose-resistance amylase regulator CcpA, C-terminal domain	(Priestia megaterium ) [TaxId: 1404 ],	SCOPe (2.08)
F [auth C]	d1rzrc1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	GalR/LacI-like bacterial regulator	Glucose-resistance amylase regulator CcpA, N-terminal domain	(Priestia megaterium ) [TaxId: 1404 ],	SCOPe (2.08)
F [auth C]	d1rzrc2	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	L-arabinose binding protein-like	Glucose-resistance amylase regulator CcpA, C-terminal domain	(Priestia megaterium ) [TaxId: 1404 ],	SCOPe (2.08)
G [auth A]	d1rzra1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	GalR/LacI-like bacterial regulator	Glucose-resistance amylase regulator CcpA, N-terminal domain	(Priestia megaterium ) [TaxId: 1404 ],	SCOPe (2.08)
G [auth A]	d1rzra2	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	L-arabinose binding protein-like	Glucose-resistance amylase regulator CcpA, C-terminal domain	(Priestia megaterium ) [TaxId: 1404 ],	SCOPe (2.08)
H [auth D]	d1rzrd1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	GalR/LacI-like bacterial regulator	Glucose-resistance amylase regulator CcpA, N-terminal domain	(Priestia megaterium ) [TaxId: 1404 ],	SCOPe (2.08)
H [auth D]	d1rzrd2	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	L-arabinose binding protein-like	Glucose-resistance amylase regulator CcpA, C-terminal domain	(Priestia megaterium ) [TaxId: 1404 ],	SCOPe (2.08)
I [auth T]	d1rzrt_	Alpha and beta proteins (a+b)	HPr-like	HPr-like	HPr-like	Histidine-containing phosphocarrier protein (HPr)	(Priestia megaterium ) [TaxId: 1404 ],	SCOPe (2.08)
J [auth L]	d1rzrl_	Alpha and beta proteins (a+b)	HPr-like	HPr-like	HPr-like	Histidine-containing phosphocarrier protein (HPr)	(Priestia megaterium ) [TaxId: 1404 ],	SCOPe (2.08)
K [auth Y]	d1rzry_	Alpha and beta proteins (a+b)	HPr-like	HPr-like	HPr-like	Histidine-containing phosphocarrier protein (HPr)	(Priestia megaterium ) [TaxId: 1404 ],	SCOPe (2.08)
L [auth S]	d1rzrs_	Alpha and beta proteins (a+b)	HPr-like	HPr-like	HPr-like	Histidine-containing phosphocarrier protein (HPr)	(Priestia megaterium ) [TaxId: 1404 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth G]	SCOP2B Superfamily	Type 1 solute binding protein-like	8043372	3000125	SCOP2B (2022-06-29)
E [auth G]	SCOP2B Superfamily	lambda C1 repressor DNA-binding domain-like	8042416	3000119	SCOP2B (2022-06-29)
F [auth C]	SCOP2B Superfamily	lambda C1 repressor DNA-binding domain-like	8042416	3000119	SCOP2B (2022-06-29)
F [auth C]	SCOP2B Superfamily	Type 1 solute binding protein-like	8043372	3000125	SCOP2B (2022-06-29)
G [auth A]	SCOP2B Superfamily	Type 1 solute binding protein-like	8043372	3000125	SCOP2B (2022-06-29)
G [auth A]	SCOP2B Superfamily	lambda C1 repressor DNA-binding domain-like	8042416	3000119	SCOP2B (2022-06-29)
H [auth D]	SCOP2B Superfamily	Type 1 solute binding protein-like	8043372	3000125	SCOP2B (2022-06-29)
H [auth D]	SCOP2B Superfamily	lambda C1 repressor DNA-binding domain-like	8042416	3000119	SCOP2B (2022-06-29)
I [auth T]	SCOP2B Superfamily	HPr-like	8043373	3000259	SCOP2B (2022-06-29)
J [auth L]	SCOP2B Superfamily	HPr-like	8043373	3000259	SCOP2B (2022-06-29)
K [auth Y]	SCOP2B Superfamily	HPr-like	8043373	3000259	SCOP2B (2022-06-29)
L [auth S]	SCOP2B Superfamily	HPr-like	8043373	3000259	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E [auth G]	LacI	e1rzrG5	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: LacI	ECOD (1.6)
E [auth G]	Peripla_BP_3	e1rzrG3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_3	ECOD (1.6)
E [auth G]	Peripla_BP_1_1st_1	e1rzrG4	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_1_1st_1	ECOD (1.6)
F [auth C]	LacI	e1rzrC5	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: LacI	ECOD (1.6)
F [auth C]	Peripla_BP_3	e1rzrC3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_3	ECOD (1.6)
F [auth C]	Peripla_BP_1_1st_1	e1rzrC2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_1_1st_1	ECOD (1.6)
G [auth A]	LacI	e1rzrA1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: LacI	ECOD (1.6)
G [auth A]	Peripla_BP_3	e1rzrA3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_3	ECOD (1.6)
G [auth A]	Peripla_BP_1_1st_1	e1rzrA4	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_1_1st_1	ECOD (1.6)
H [auth D]	LacI	e1rzrD5	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: LacI	ECOD (1.6)
H [auth D]	Peripla_BP_3	e1rzrD3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_3	ECOD (1.6)
H [auth D]	Peripla_BP_1_1st_1	e1rzrD2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_1_1st_1	ECOD (1.6)
I [auth T]	PTS-HPr	e1rzrT1	A: a+b two layers	X: HPr-like (From Topology)	H: HPr-like (From Topology)	T: HPr-like	F: PTS-HPr	ECOD (1.6)
J [auth L]	PTS-HPr	e1rzrL1	A: a+b two layers	X: HPr-like (From Topology)	H: HPr-like (From Topology)	T: HPr-like	F: PTS-HPr	ECOD (1.6)
K [auth Y]	PTS-HPr	e1rzrY1	A: a+b two layers	X: HPr-like (From Topology)	H: HPr-like (From Topology)	T: HPr-like	F: PTS-HPr	ECOD (1.6)
L [auth S]	PTS-HPr	e1rzrS1	A: a+b two layers	X: HPr-like (From Topology)	H: HPr-like (From Topology)	T: HPr-like	F: PTS-HPr	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E [auth G]	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
E [auth G]	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
F [auth C]	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
F [auth C]	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
G [auth A]	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
G [auth A]	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
H [auth D]	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
H [auth D]	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
I [auth T]	3.30.1340.10	Alpha Beta	2-Layer Sandwich	Histidine-containing Protein	Chain: A	CATH (4.3.0)
J [auth L]	3.30.1340.10	Alpha Beta	2-Layer Sandwich	Histidine-containing Protein	Chain: A	CATH (4.3.0)
K [auth Y]	3.30.1340.10	Alpha Beta	2-Layer Sandwich	Histidine-containing Protein	Chain: A	CATH (4.3.0)
L [auth S]	3.30.1340.10	Alpha Beta	2-Layer Sandwich	Histidine-containing Protein	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth G], F [auth C], G [auth A]	PF13377	Periplasmic binding protein-like domain (Peripla_BP_3)	Periplasmic binding protein-like domain	This domain is found in a variety of transcriptional regulatory proteins. It is related to bacterial periplasmic binding proteins, although this domain is unlikely to be found in the periplasm. This domain acts as a sensor binding small molecule liga ...	This domain is found in a variety of transcriptional regulatory proteins. It is related to bacterial periplasmic binding proteins, although this domain is unlikely to be found in the periplasm. This domain acts as a sensor binding small molecule ligands that the DNA-binding domain responds to. This domain recognises Sugars, sugar phosphates, sugar acids and purines (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).	Domain
E [auth G], F [auth C], G [auth A]	PF00356	Bacterial regulatory proteins, lacI family (LacI)	Bacterial regulatory proteins, lacI family	-	Domain
H [auth D]	PF13377	Periplasmic binding protein-like domain (Peripla_BP_3)	Periplasmic binding protein-like domain	This domain is found in a variety of transcriptional regulatory proteins. It is related to bacterial periplasmic binding proteins, although this domain is unlikely to be found in the periplasm. This domain acts as a sensor binding small molecule liga ...	This domain is found in a variety of transcriptional regulatory proteins. It is related to bacterial periplasmic binding proteins, although this domain is unlikely to be found in the periplasm. This domain acts as a sensor binding small molecule ligands that the DNA-binding domain responds to. This domain recognises Sugars, sugar phosphates, sugar acids and purines (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).	Domain
H [auth D]	PF00356	Bacterial regulatory proteins, lacI family (LacI)	Bacterial regulatory proteins, lacI family	-	Domain
I [auth T], J [auth L], K [auth Y], L [auth S]	PF00381	PTS HPr component phosphorylation site (PTS-HPr)	PTS HPr component phosphorylation site	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth H], C [auth E]	5'-D(CPTPGPAPAPAPGPCPGPCPTPAPAPCPAPG)-3'	-	-	-
B [auth R], D [auth B]	5'-D(CPTPGPTPTPAPGPCPGPCPTPTPTPCPAPG)-3'	-	-	-
E [auth G], F [auth C], G [auth A]	Glucose-resistance amylase regulator	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding transcription regulator activity DNA-binding transcription factor activity	-	-
H [auth D]	Glucose-resistance amylase regulator	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding transcription regulator activity DNA-binding transcription factor activity	-	-
I [auth T], J [auth L], K [auth Y], L [auth S]	Phosphocarrier protein HPr	-	import into cell phosphoenolpyruvate-dependent sugar phosphotransferase system transport import across plasma membrane carbohydrate import across plasma membrane carbohydrate transport establishment of localization transmembrane transport localization cellular process carbohydrate transmembrane transport	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth G], F [auth C], G [auth A]	IPR046335	Transcriptional regulator LacI/GalR-like, sensor domain	Domain
E [auth G], F [auth C], G [auth A]	IPR000843	LacI-type HTH domain	Domain
E [auth G], F [auth C], G [auth A]	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
E [auth G], F [auth C], G [auth A]	IPR006377	Catabolite control protein A	Family
E [auth G], F [auth C], G [auth A]	IPR010982	Lambda repressor-like, DNA-binding domain superfamily	Homologous Superfamily
H [auth D]	IPR046335	Transcriptional regulator LacI/GalR-like, sensor domain	Domain
H [auth D]	IPR000843	LacI-type HTH domain	Domain
H [auth D]	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
H [auth D]	IPR006377	Catabolite control protein A	Family
H [auth D]	IPR010982	Lambda repressor-like, DNA-binding domain superfamily	Homologous Superfamily
I [auth T], J [auth L], K [auth Y], L [auth S]	IPR000032	Phosphocarrier protein HPr-like	Domain
I [auth T], J [auth L], K [auth Y], L [auth S]	IPR002114	Phosphotransferase system, HPr serine phosphorylation site	PTM
I [auth T], J [auth L], K [auth Y], L [auth S]	IPR050399	Phosphocarrier protein HPr	Family
I [auth T], J [auth L], K [auth Y], L [auth S]	IPR035895	HPr-like superfamily	Homologous Superfamily
I [auth T], J [auth L], K [auth Y], L [auth S]	IPR001020	Phosphotransferase system, HPr histidine phosphorylation site	PTM

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E [auth G], F [auth C], G [auth A]	MSE	Parent Component: MET
H [auth D]	MSE	Parent Component: MET
I [auth T], J [auth L], K [auth Y], L [auth S]	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.