1XP4 | pdb_00001xp4

Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d1xp4d1	All beta proteins	Penicillin-binding protein associated domain	Penicillin-binding protein associated domain	PBP5 C-terminal domain-like	D,D-carboxypeptidase DacA, C-terminal domain	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
D	d1xp4d2	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	beta-Lactamase/D-ala carboxypeptidase	D,D-carboxypeptidase DacA, N-terminal domain	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
C	d1xp4c1	All beta proteins	Penicillin-binding protein associated domain	Penicillin-binding protein associated domain	PBP5 C-terminal domain-like	D,D-carboxypeptidase DacA, C-terminal domain	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
C	d1xp4c2	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	beta-Lactamase/D-ala carboxypeptidase	D,D-carboxypeptidase DacA, N-terminal domain	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
B	d1xp4b1	All beta proteins	Penicillin-binding protein associated domain	Penicillin-binding protein associated domain	PBP5 C-terminal domain-like	D,D-carboxypeptidase DacA, C-terminal domain	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
B	d1xp4b2	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	beta-Lactamase/D-ala carboxypeptidase	D,D-carboxypeptidase DacA, N-terminal domain	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
A	d1xp4a1	All beta proteins	Penicillin-binding protein associated domain	Penicillin-binding protein associated domain	PBP5 C-terminal domain-like	D,D-carboxypeptidase DacA, C-terminal domain	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
A	d1xp4a2	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	beta-Lactamase/D-ala carboxypeptidase	D,D-carboxypeptidase DacA, N-terminal domain	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8044099	3001604	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Penicillin-binding protein associated domain	8044098	3002006	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8044099	3001604	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8044099	3001604	SCOP2B (2022-06-29)
A	SCOP2 Family	PBP5 C-terminal domain-like	8031720	4003008	SCOP2 (2022-06-29)
A	SCOP2 Family	beta-Lactamase/D-ala carboxypeptidase	8031721	4002685	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Penicillin-binding protein associated domain	8044098	3002006	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	beta-lactamase/transpeptidase-like	8044099	3001604	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	MS_channel_2nd	e1xp4D4	A: alpha bundles	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: MS_channel_2nd	ECOD (develop294)
D	PI3K_C2	e1xp4D2	A: alpha bundles	X: YrdC/RibB	H: SH3	T: SH3	F: PI3K_C2	ECOD (develop294)
C	Ricin_B_lectin, RicinB_lectin_2	e1xp4C1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Ricin_B_lectin, RicinB_lectin_2	ECOD (develop294)
C	Ion_trans_2	e1xp4C2	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Ion_trans_2	ECOD (develop294)
C	Transpeptidase	e1xp4C3	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Transpeptidase	ECOD (develop294)
B	MS_channel_2nd	e1xp4B4	A: alpha bundles	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: MS_channel_2nd	ECOD (develop294)
A	PBP5_C	e1xp4A1	A: beta sandwiches	X: Penicillin-binding protein associated domain	H: Penicillin-binding protein associated domain	T: Penicillin-binding protein associated domain	F: PBP5_C	ECOD (develop294)
A	Beta-lactamase	e1xp4A2	A: a+b two layers	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase	ECOD (develop294)
A	Transpeptidase	e1xp4A3	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Transpeptidase	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
D	2.60.410.10	Mainly Beta	Sandwich	Peptidoglycan synthesis regulatory factor (PBP3), Domain 2	D-Ala-D-Ala carboxypeptidase, C-terminal domain	CATH (4.3.0)
C	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
C	2.60.410.10	Mainly Beta	Sandwich	Peptidoglycan synthesis regulatory factor (PBP3), Domain 2	D-Ala-D-Ala carboxypeptidase, C-terminal domain	CATH (4.3.0)
B	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
B	2.60.410.10	Mainly Beta	Sandwich	Peptidoglycan synthesis regulatory factor (PBP3), Domain 2	D-Ala-D-Ala carboxypeptidase, C-terminal domain	CATH (4.3.0)
A	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
A	2.60.410.10	Mainly Beta	Sandwich	Peptidoglycan synthesis regulatory factor (PBP3), Domain 2	D-Ala-D-Ala carboxypeptidase, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF07943	Penicillin-binding protein 5, C-terminal domain (PBP5_C)	Penicillin-binding protein 5, C-terminal domain	Penicillin-binding protein 5 expressed by E. coli (Swiss:P04287) functions as a D-alanyl-D-alanine carboxypeptidase. It is composed of two domains that are oriented at approximately right angles to each other. The N-terminal domain (Pfam:PF00768) is ...	Penicillin-binding protein 5 expressed by E. coli (Swiss:P04287) functions as a D-alanyl-D-alanine carboxypeptidase. It is composed of two domains that are oriented at approximately right angles to each other. The N-terminal domain (Pfam:PF00768) is the catalytic domain. The C-terminal domain featured in this family is organised into a sandwich of two anti-parallel beta-sheets, and has a relatively hydrophobic surface as compared to the N-terminal domain. Its precise function is unknown; it may mediate interactions with other cell wall-synthesising enzymes, thus allowing the protein to be recruited to areas of active cell wall synthesis. It may also function as a linker domain that positions the active site in the catalytic domain closer to the peptidoglycan layer, to allow it to interact with cell wall peptides [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	D-alanyl-D-alanine carboxypeptidase	serine-type exopeptidase activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity hydrolase activity serine-type D-Ala-D-Ala carboxypeptidase activity serine-type carboxypeptidase activity serine-type peptidase activity exopeptidase activity catalytic activity carboxypeptidase activity	developmental process regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis cell wall organization or biogenesis developmental process regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis cell wall organization or biogenesis glycosaminoglycan metabolic process carbohydrate derivative metabolic process macromolecule biosynthetic process cellular component biogenesis peptidoglycan biosynthetic process cell wall biogenesis biosynthetic process cell wall macromolecule biosynthetic process aminoglycan metabolic process peptidoglycan metabolic process aminoglycan biosynthetic process cellular process metabolic process glycosaminoglycan biosynthetic process cellular component organization or biogenesis macromolecule metabolic process cell wall macromolecule metabolic process proteolysis primary metabolic process protein metabolic process cellular component organization cell wall organization external encapsulating structure organization	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR037167	D-Ala-D-Ala carboxypeptidase, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR012907	Peptidase S11, D-Ala-D-Ala carboxypeptidase A, C-terminal	Domain
A, B, C, D	IPR018044	Peptidase S11, D-alanyl-D-alanine carboxypeptidase A	Family
A, B, C, D	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
A, B, C, D	IPR015956	Penicillin-binding protein, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR001967	Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal	Domain

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.