3L31

Crystal structure of the CBS and DRTGG domains of the regulatory region of Clostridium perfringens pyrophosphatase complexed with the inhibitor, AMP

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	HprK N-terminal domain-like	8057769	3001032	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CBS-domain pair	8057770	3000123	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CBS-domain pair	8057770	3000123	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HprK N-terminal domain-like	8057769	3001032	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)
A	IMPDH_2nd_1	e3l31A1	A: a+b duplicates or obligate multimers	X: CBS-domain (From Topology)	H: CBS-domain (From Topology)	T: CBS-domain	F: IMPDH_2nd_1	ECOD (1.6)
A	DRTGG	e3l31A2	A: a/b three-layered sandwiches	X: MurF and HprK N-domain-like (From Topology)	H: MurF and HprK N-domain-like (From Topology)	T: MurF and HprK N-domain-like	F: DRTGG	ECOD (1.6)
B	IMPDH_2nd_1	e3l31B1	A: a+b duplicates or obligate multimers	X: CBS-domain (From Topology)	H: CBS-domain (From Topology)	T: CBS-domain	F: IMPDH_2nd_1	ECOD (1.6)
B	DRTGG	e3l31B2	A: a/b three-layered sandwiches	X: MurF and HprK N-domain-like (From Topology)	H: MurF and HprK N-domain-like (From Topology)	T: MurF and HprK N-domain-like	F: DRTGG	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.580.10	Alpha Beta	Roll	CBS-domain	CBS-domain	CATH (4.3.0)
A	3.40.1390.20	Alpha Beta	3-Layer(aba) Sandwich	Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase	Chain: A, domain 1	CATH (4.3.0)
B	3.10.580.10	Alpha Beta	Roll	CBS-domain	CBS-domain	CATH (4.3.0)
B	3.40.1390.20	Alpha Beta	3-Layer(aba) Sandwich	Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase	Chain: A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF07085	DRTGG domain (DRTGG)	DRTGG domain	This presumed domain is about 120 amino acids in length. It is found associated with CBS domains Pfam:PF00571, as well as the CbiA domain Pfam:PF01656. The function of this domain is unknown. It is named the DRTGG domain after some of the most conse ...	This presumed domain is about 120 amino acids in length. It is found associated with CBS domains Pfam:PF00571, as well as the CbiA domain Pfam:PF01656. The function of this domain is unknown. It is named the DRTGG domain after some of the most conserved residues. This domain may be very distantly related to a pair of CBS domains. There are no significant sequence similarities, but its length and association with CBS domains supports this idea (Bateman A, pers. obs.).	Domain
A, B	PF00571	CBS domain (CBS)	CBS domain	CBS domains are small intracellular modules that pair together to form a stable globular domain [2]. This family represents a single CBS domain. Pairs of these domains have been termed a Bateman domain [6]. CBS domains have been shown to bind ligands ...	CBS domains are small intracellular modules that pair together to form a stable globular domain [2]. This family represents a single CBS domain. Pairs of these domains have been termed a Bateman domain [6]. CBS domains have been shown to bind ligands with an adenosyl group such as AMP, ATP and S-AdoMet [5]. CBS domains are found attached to a wide range of other protein domains suggesting that CBS domains may play a regulatory role making proteins sensitive to adenosyl carrying ligands. The region containing the CBS domains in Cystathionine-beta synthase is involved in regulation by S-AdoMet [4]. CBS domain pairs from AMPK bind AMP or ATP [5]. The CBS domains from IMPDH and the chloride channel CLC2 bind ATP [5].	Domain
A, B	PF01368	DHH family, N-terminal domain (DHH)	DHH family, N-terminal domain	It is predicted that this family of proteins all perform a phosphoesterase function. This domain is found at the N-terminal of the single stranded DNA exonuclease RecJ. It shows an alpha-beta configuration [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Probable manganase-dependent inorganic pyrophosphatase	cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding manganese ion binding pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity inorganic diphosphate phosphatase activity hydrolase activity, acting on acid anhydrides catalytic activity cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding manganese ion binding pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity inorganic diphosphate phosphatase activity hydrolase activity, acting on acid anhydrides catalytic activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding AMP binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding	phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR046342	CBS domain superfamily	Homologous Superfamily
A, B	IPR010766	DRTGG	Domain
A, B	IPR038222	DHHA2 domain superfamily	Homologous Superfamily
A, B	IPR001667	DDH domain	Domain
A, B	IPR000644	CBS domain	Domain
A, B	IPR004097	DHHA2 domain	Domain
A, B	IPR038763	DHH phosphoesterase superfamily	Homologous Superfamily
A, B	IPR028979	HPr(Ser) kinase/phosphorylase-like, N-terminal domain superfamily	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.