1K47 | pdb_00001k47

Crystal Structure of the Streptococcus pneumoniae Phosphomevalonate Kinase (PMK)

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)
F	d1k47f1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	GHMP Kinase, N-terminal domain	Phosphomevalonate kinase (PMK)	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
F	d1k47f2	Alpha and beta proteins (a+b)	Ferredoxin-like	GHMP Kinase, C-terminal domain	Phosphomevalonate kinase (PMK)	Phosphomevalonate kinase (PMK)	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
F	d1k47f3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
E	d1k47e1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	GHMP Kinase, N-terminal domain	Phosphomevalonate kinase (PMK)	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
E	d1k47e2	Alpha and beta proteins (a+b)	Ferredoxin-like	GHMP Kinase, C-terminal domain	Phosphomevalonate kinase (PMK)	Phosphomevalonate kinase (PMK)	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
E	d1k47e3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
D	d1k47d1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	GHMP Kinase, N-terminal domain	Phosphomevalonate kinase (PMK)	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
D	d1k47d2	Alpha and beta proteins (a+b)	Ferredoxin-like	GHMP Kinase, C-terminal domain	Phosphomevalonate kinase (PMK)	Phosphomevalonate kinase (PMK)	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
D	d1k47d3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
C	d1k47c1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	GHMP Kinase, N-terminal domain	Phosphomevalonate kinase (PMK)	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
C	d1k47c2	Alpha and beta proteins (a+b)	Ferredoxin-like	GHMP Kinase, C-terminal domain	Phosphomevalonate kinase (PMK)	Phosphomevalonate kinase (PMK)	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
C	d1k47c3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
B	d1k47b1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	GHMP Kinase, N-terminal domain	Phosphomevalonate kinase (PMK)	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
B	d1k47b2	Alpha and beta proteins (a+b)	Ferredoxin-like	GHMP Kinase, C-terminal domain	Phosphomevalonate kinase (PMK)	Phosphomevalonate kinase (PMK)	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
B	d1k47b3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
A	d1k47a1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	GHMP Kinase, N-terminal domain	Phosphomevalonate kinase (PMK)	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
A	d1k47a2	Alpha and beta proteins (a+b)	Ferredoxin-like	GHMP Kinase, C-terminal domain	Phosphomevalonate kinase (PMK)	Phosphomevalonate kinase (PMK)	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
A	d1k47a3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(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)
F	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8040027	3000100	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	GHMP Kinase, C-terminal domain	8040029	3001245	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8040027	3000100	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	GHMP Kinase, C-terminal domain	8040029	3001245	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	GHMP Kinase, C-terminal domain	8040029	3001245	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8040027	3000100	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8040027	3000100	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GHMP Kinase, C-terminal domain	8040029	3001245	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8040027	3000100	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GHMP Kinase, C-terminal domain	8040029	3001245	SCOP2B (2022-06-29)
A	SCOP2 Family	GHMP Kinase, N-terminal domain	8027648	4000959	SCOP2 (2022-06-29)
A	SCOP2 Family	Phosphomevalonate kinase (PMK)	8027650	4002670	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribosomal protein S5 domain 2-like	8040027	3000100	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GHMP Kinase, C-terminal domain	8040029	3001245	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)
F	Propep_M14	e1k47F1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Propep_M14	ECOD (v294.1)
F	Staphylokinase	e1k47F2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Staphylokinase	ECOD (v294.1)
E	Propep_M14	e1k47E1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Propep_M14	ECOD (v294.1)
E	Staphylokinase	e1k47E2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Staphylokinase	ECOD (v294.1)
D	Propep_M14	e1k47D1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Propep_M14	ECOD (v294.1)
D	Staphylokinase	e1k47D2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Staphylokinase	ECOD (v294.1)
C	Propep_M14	e1k47C1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Propep_M14	ECOD (v294.1)
C	Staphylokinase	e1k47C2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Staphylokinase	ECOD (v294.1)
B	Propep_M14	e1k47B1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Propep_M14	ECOD (v294.1)
B	Staphylokinase	e1k47B2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Staphylokinase	ECOD (v294.1)
A	GHMP_kinases_C	e1k47A1	A: a+b two layers	X: Alpha-beta plaits	H: GHMP Kinase, C-terminal domain	T: GHMP Kinase, C-terminal domain	F: GHMP_kinases_C	ECOD (v294.1)
A	GHMP_kinases_N	e1k47A2	A: a+b two layers	X: Ribosomal protein S5 domain 2-like	H: Ribosomal protein S5 domain 2-like	T: Ribosomal protein S5 domain 2-like	F: GHMP_kinases_N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
F	3.30.70.890	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	GHMP kinase, C-terminal domain	CATH (4.3.0)
E	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
E	3.30.70.890	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	GHMP kinase, C-terminal domain	CATH (4.3.0)
D	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
D	3.30.70.890	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	GHMP kinase, C-terminal domain	CATH (4.3.0)
C	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
C	3.30.70.890	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	GHMP kinase, C-terminal domain	CATH (4.3.0)
B	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
B	3.30.70.890	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	GHMP kinase, C-terminal domain	CATH (4.3.0)
A	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
A	3.30.70.890	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	GHMP kinase, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF08544	GHMP kinases C terminal (GHMP_kinases_C)	GHMP kinases C terminal	This family includes homoserine kinases, galactokinases and mevalonate kinases.	Domain
A, B, C, D, E A, B, C, D, E, F	PF00288	GHMP kinases N terminal domain (GHMP_kinases_N)	GHMP kinases N terminal domain	This entry represents a conserved domain with a Gly/Ser-rich region found in galacto-, homoserine, mevalonate and phosphomevalonate kinases (GHMP) which is involved in the binding of ATP [1,2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	phosphomevalonate kinase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding kinase activity phosphomevalonate kinase activity transferase activity catalytic activity phosphotransferase activity, phosphate group as acceptor transferase activity, transferring phosphorus-containing groups cation binding metal ion binding	isopentenyl diphosphate biosynthetic process lipid biosynthetic process acetyl-CoA metabolic process phospholipid metabolic process nucleobase-containing compound metabolic process acyl-CoA metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process sulfur compound metabolic process small molecule metabolic process phosphorus metabolic process nucleoside phosphate metabolic process isoprenoid biosynthetic process primary metabolic process isopentenyl diphosphate biosynthetic process lipid biosynthetic process acetyl-CoA metabolic process phospholipid metabolic process nucleobase-containing compound metabolic process acyl-CoA metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process sulfur compound metabolic process small molecule metabolic process phosphorus metabolic process nucleoside phosphate metabolic process isoprenoid biosynthetic process primary metabolic process phospholipid biosynthetic process purine-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process metabolic process cellular process isopentenyl diphosphate biosynthetic process, mevalonate pathway lipid metabolic process isoprenoid metabolic process isopentenyl diphosphate metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR006204	GHMP kinase N-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR035102	Phosphomevalonate kinase	Family
A, B, C, D, E A, B, C, D, E, F	IPR013750	GHMP kinase, C-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR005917	Phosphomevalonate kinase, bacteria	Family
A, B, C, D, E A, B, C, D, E, F	IPR036554	GHMP kinase, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR014721	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Homologous Superfamily

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.