5KH2 | pdb_00005kh2

Crystal Structure of Steptococcus pneumoniae Undecaprenyl pyrophosphate Synthase (UPPS)

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	d5kh2d_	Alpha and beta proteins (a/b)	Undecaprenyl diphosphate synthase	Undecaprenyl diphosphate synthase	automated matches	automated matches	(Streptococcus pneumoniae TIGR4 ) [TaxId: 170187 ],	SCOPe (2.08)
C	d5kh2c_	Alpha and beta proteins (a/b)	Undecaprenyl diphosphate synthase	Undecaprenyl diphosphate synthase	automated matches	automated matches	(Streptococcus pneumoniae TIGR4 ) [TaxId: 170187 ],	SCOPe (2.08)
B	d5kh2b_	Alpha and beta proteins (a/b)	Undecaprenyl diphosphate synthase	Undecaprenyl diphosphate synthase	automated matches	automated matches	(Streptococcus pneumoniae TIGR4 ) [TaxId: 170187 ],	SCOPe (2.08)
A	d5kh2a_	Alpha and beta proteins (a/b)	Undecaprenyl diphosphate synthase	Undecaprenyl diphosphate synthase	automated matches	automated matches	(Streptococcus pneumoniae TIGR4 ) [TaxId: 170187 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Undecaprenyl diphosphate synthase	8067712	3000594	SCOP2B (2022-06-29)
C	SCOP2 Family	Undecaprenyl diphosphate synthase-like	8067711	4003318	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Undecaprenyl diphosphate synthase	8067712	3000594	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Undecaprenyl diphosphate synthase	8067712	3000594	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Undecaprenyl diphosphate synthase	8067712	3000594	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)
D		e5kh2D1	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: TGS	F:	ECOD (20:10:01)
C		e5kh2C1	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: TGS	F:	ECOD (20:10:01)
B		e5kh2B1	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: TGS	F:	ECOD (20:10:01)
A		e5kh2A1	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: TGS	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.1180.10	Alpha Beta	3-Layer(aba) Sandwich	Undecaprenyl pyrophosphate synthetase	Decaprenyl diphosphate synthase-like	CATH (4.3.0)
C	3.40.1180.10	Alpha Beta	3-Layer(aba) Sandwich	Undecaprenyl pyrophosphate synthetase	Decaprenyl diphosphate synthase-like	CATH (4.3.0)
B	3.40.1180.10	Alpha Beta	3-Layer(aba) Sandwich	Undecaprenyl pyrophosphate synthetase	Decaprenyl diphosphate synthase-like	CATH (4.3.0)
A	3.40.1180.10	Alpha Beta	3-Layer(aba) Sandwich	Undecaprenyl pyrophosphate synthetase	Decaprenyl diphosphate synthase-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01255	Putative undecaprenyl diphosphate synthase (Prenyltransf)	Putative undecaprenyl diphosphate synthase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Isoprenyl transferase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding manganese ion binding transition metal ion binding prenyl diphosphate synthase activity ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] activity prenyltransferase activity ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding manganese ion binding transition metal ion binding prenyl diphosphate synthase activity ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] activity prenyltransferase activity ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups catalytic activity	polyprenol metabolic process polyprenol biosynthetic process small molecule biosynthetic process isoprenoid biosynthetic process lipid biosynthetic process alcohol metabolic process primary metabolic process biosynthetic process alcohol biosynthetic process small molecule metabolic process metabolic process cellular process isoprenoid metabolic process lipid metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR018520	Di-trans-poly-cis-decaprenylcistransferase-like, conserved site	Conserved Site
A, B, C, D	IPR036424	Decaprenyl diphosphate synthase-like superfamily	Homologous Superfamily
A, B, C, D	IPR001441	Decaprenyl diphosphate synthase-like	Family

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.