5IIT

Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1

Present annotations:

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Product Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Macro domain-like	8036145	3000458	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Macro domain-like	8036145	3000458	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Macro domain-like	8036145	3000458	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Macro domain-like	8036145	3000458	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	SPX	e5iitA2	A: alpha bundles	X: SPX domain (From Topology)	H: SPX domain (From Topology)	T: SPX domain	F: SPX	ECOD (1.6)
A	Macro	e5iitA1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
B	SPX	e5iitB2	A: alpha bundles	X: SPX domain (From Topology)	H: SPX domain (From Topology)	T: SPX domain	F: SPX	ECOD (1.6)
B	Macro	e5iitB1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
C	SPX	e5iitC2	A: alpha bundles	X: SPX domain (From Topology)	H: SPX domain (From Topology)	T: SPX domain	F: SPX	ECOD (1.6)
C	Macro	e5iitC1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
D	SPX	e5iitD2	A: alpha bundles	X: SPX domain (From Topology)	H: SPX domain (From Topology)	T: SPX domain	F: SPX	ECOD (1.6)
D	Macro	e5iitD1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Identifier	Description	Comments	Source
A, B, C, D	PF01661	Macro domain (Macro)	Macro domain	The Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose (an NAD metabolite) or related ligands. Binding to ADP-ribose could be either covalent or non-covalent [1]: in certain cases it is believed to bind non-covalently ...	The Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose (an NAD metabolite) or related ligands. Binding to ADP-ribose could be either covalent or non-covalent [1]: in certain cases it is believed to bind non-covalently [2]; while in other cases (such as Aprataxin) it appears to bind both non-covalently through a zinc finger motif, and covalently through a separate region of the protein [3]. This domain is found in a number of otherwise unrelated proteins. It is found at the C-terminus of the macro-H2A histone protein 4 and also in the non-structural proteins of several types of ssRNA viruses such as NSP3 from alpha-viruses and coronaviruses. This domain is also found on its own in a family of proteins from bacteria, archaebacteria and eukaryotes. The 3D structure of the SARS-CoV Macro domain has a mixed alpha/beta fold consisting of a central seven-stranded twisted mixed beta sheet sandwiched between two alpha helices on one face, and three on the other. The final alpha-helix, located on the edge of the central beta-sheet, forms the C terminus of the protein [4]. The crystal structure of AF1521 (a Macro domain-only protein from Archaeoglobus fulgidus) has also been reported and compared with other Macro domain containing proteins. Several Macro domain only proteins are shorter than AF1521, and appear to lack either the first strand of the beta-sheet or the C-terminal helix 5. Well conserved residues form a hydrophobic cleft and cluster around the AF1521-ADP-ribose binding site [5].	Domain

Gene Product Annotation Gene Product Annotation

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Vacuolar transporter chaperone 4,Core histone macro-H2A.1	nucleic acid binding DNA binding chromatin binding binding chromatin DNA binding protein-containing complex binding organic cyclic compound binding heterocyclic compound binding double-stranded DNA binding double-stranded methylated DNA binding protein binding enzyme binding nucleosome binding nucleosomal DNA binding promoter-specific chromatin binding protein heterodimerization activity protein dimerization activity kinase binding protein kinase binding enzyme inhibitor activity protein kinase inhibitor activity kinase regulator activity kinase inhibitor activity protein kinase regulator activity enzyme regulator activity protein serine/threonine kinase inhibitor activity molecular function regulator activity molecular function inhibitor activity structural molecule activity structural constituent of chromatin calmodulin binding catalytic activity polyphosphate kinase activity kinase activity transferase activity transferase activity, transferring phosphorus-containing groups phosphotransferase activity, phosphate group as acceptor		extracellular region extracellular space vesicle organelle membrane-bounded organelle extracellular organelle extracellular membrane-bounded organelle extracellular exosome cellular anatomical entity extracellular vesicle intracellular anatomical structure nucleus nucleolus membrane-enclosed lumen nuclear lumen non-membrane-bounded organelle intracellular organelle intracellular membrane-bounded organelle intracellular non-membrane-bounded organelle organelle lumen intracellular organelle lumen nucleoplasm cell periphery cytoplasm endoplasmic reticulum endomembrane system membrane protein-containing complex vacuolar transporter chaperone complex membrane protein complex intracellular protein-containing complex

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.