S100 Family: 3.10.28.10.9.1.1.1

Representative domain: 1dfaA03

Classification Lineage (3.10.28.10.9.1.1.1)

CATH Code	Level Description	Links
3	Alpha Beta
3.10	Roll
3.10.28	Endonuclease I-creI
3.10.28.10	Homing endonucleases	Gene3D
3.10.28.10.9
3.10.28.10.9.1
3.10.28.10.9.1.1
3.10.28.10.9.1.1.1

Summary of Non-Redundant Representatives


-	-	-	-	-	-	-	-	8

Non-Redundant Representatives (8)
Functional Families
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What is a Non-Redundant Representative?

CATH is a tree-like organisation of nodes that begins with the class node (i.e. the first branch-point of the tree) and ends with the domain nodes (i.e. the leaves of the tree). Each node below the class have a parent that they belong to, e.g. the parent of the H level (Homologous superfamily) is the T (Topology). Additionally, each node above the domains have child nodes that belong to them, e.g. the child nodes of a given H (Homologous superfamily) level are the S35 families (domains clustered at > 35% sequence identity).

S100 Count Entries in S100 Family 3.10.28.10.9.1.1.1 (8)

CATH code	Domain ID	Keywords
3.10.28.10.9.1.1.1.1	1dfaA03	V-type proton ATPase catalytic subunit A, Oxidative phosphorylation, proton-transporting ATPase activity, rotational mechanism, Saccharomyces cerevisiae, V-type H+-transporting ATPase subunit A [EC:3.6.3.14], vacuolar acidification, protein binding, Acting on ester bonds., Metabolic pathways, H(+)-transporting two-sector ATPase., intron homing, vacuolar proton-transporting V-type ATPase, V1 domain, cellular protein metabolic process, fungal-type vacuole membrane, endodeoxyribonuclease activity
3.10.28.10.9.1.1.1.2	1ef0A03	V-type H+-transporting ATPase subunit A [EC:3.6.3.14], Saccharomyces cerevisiae, proton-transporting ATPase activity, rotational mechanism, Oxidative phosphorylation, V-type proton ATPase catalytic subunit A, vacuolar proton-transporting V-type ATPase, V1 domain, intron homing, cellular protein metabolic process, endodeoxyribonuclease activity, fungal-type vacuole membrane, protein binding, vacuolar acidification, Metabolic pathways, H(+)-transporting two-sector ATPase., Acting on ester bonds.
3.10.28.10.9.1.1.1.3	1jvaB03	Oxidative phosphorylation, V-type proton ATPase catalytic subunit A, proton-transporting ATPase activity, rotational mechanism, Saccharomyces cerevisiae, V-type H+-transporting ATPase subunit A [EC:3.6.3.14], Acting on ester bonds., Metabolic pathways, H(+)-transporting two-sector ATPase., vacuolar acidification, protein binding, endodeoxyribonuclease activity, cellular protein metabolic process, fungal-type vacuole membrane, intron homing, vacuolar proton-transporting V-type ATPase, V1 domain
3.10.28.10.9.1.1.1.4	1jvaA03	cellular protein metabolic process, endodeoxyribonuclease activity, fungal-type vacuole membrane, vacuolar proton-transporting V-type ATPase, V1 domain, intron homing, Metabolic pathways, H(+)-transporting two-sector ATPase., Acting on ester bonds., protein binding, vacuolar acidification, V-type H+-transporting ATPase subunit A [EC:3.6.3.14], Saccharomyces cerevisiae, proton-transporting ATPase activity, rotational mechanism, Oxidative phosphorylation, V-type proton ATPase catalytic subunit A
3.10.28.10.9.1.1.1.5	1vdeA03	vacuolar proton-transporting V-type ATPase, V1 domain, intron homing, fungal-type vacuole membrane, cellular protein metabolic process, endodeoxyribonuclease activity, protein binding, vacuolar acidification, Metabolic pathways, H(+)-transporting two-sector ATPase., Acting on ester bonds., V-type H+-transporting ATPase subunit A [EC:3.6.3.14], Saccharomyces cerevisiae, proton-transporting ATPase activity, rotational mechanism, V-type proton ATPase catalytic subunit A, Oxidative phosphorylation
3.10.28.10.9.1.1.1.6	1vdeB03	proton-transporting ATPase activity, rotational mechanism, V-type proton ATPase catalytic subunit A, Oxidative phosphorylation, V-type H+-transporting ATPase subunit A [EC:3.6.3.14], Saccharomyces cerevisiae, Metabolic pathways, H(+)-transporting two-sector ATPase., Acting on ester bonds., protein binding, vacuolar acidification, fungal-type vacuole membrane, endodeoxyribonuclease activity, cellular protein metabolic process, vacuolar proton-transporting V-type ATPase, V1 domain, intron homing
3.10.28.10.9.1.1.1.7	1um2B03	cellular protein metabolic process, fungal-type vacuole membrane, endodeoxyribonuclease activity, intron homing, vacuolar proton-transporting V-type ATPase, V1 domain, Acting on ester bonds., Metabolic pathways, H(+)-transporting two-sector ATPase., vacuolar acidification, protein binding, Saccharomyces cerevisiae, V-type H+-transporting ATPase subunit A [EC:3.6.3.14], Oxidative phosphorylation, V-type proton ATPase catalytic subunit A, proton-transporting ATPase activity, rotational mechanism
3.10.28.10.9.1.1.1.8	1um2A03	Saccharomyces cerevisiae, V-type H+-transporting ATPase subunit A [EC:3.6.3.14], V-type proton ATPase catalytic subunit A, Oxidative phosphorylation, proton-transporting ATPase activity, rotational mechanism, endodeoxyribonuclease activity, fungal-type vacuole membrane, cellular protein metabolic process, intron homing, vacuolar proton-transporting V-type ATPase, V1 domain, Acting on ester bonds., Metabolic pathways, H(+)-transporting two-sector ATPase., vacuolar acidification, protein binding

The information on Functional Families (FunFams) is currently being updated and will be released by the end of March 2012. The pages will include the following features:

Multiple alignments for each functional family
Representative structure for each functional with known catalytic and interface residues highlighted, along with conserved residues predicted by scorecons
Detailed functional information on diversity and conservation within Functional families
Multi-domain architectures

In the meantime, please find a summary of information on the FunFams and protein networks within this superfamily on the Gene3D pages:

http://gene3d.biochem.ucl.ac.uk/superfamily/?accession=3.10.28.10.9.1.1.1

What is a Non-Redundant Representative?

Why can't I have a multiple structural alignment of the whole superfamily?

The simple answer is that some of the larger superfamilies in CATH comprise relatives which are very structurally diverse, having different secondary structure embellishments. Attempting to provide a global alignment of all domains in the superfamily would result in poor quality alignments. As a result, structural alignments in CATH are generated by first clustering together the structures that have at least some recognisable structural similarity using a normalised RMSD score (SIMAX = RMSDxNumber of residues in the largest domain/number of aligned residues) less than a given cutoff.

What is an Close Structural Cluster?

A Close Structural Cluster describes a cluster of two or more CATH domains that have been grouped together due to their close structural similarity (SIMAX score < 5Å where SIMAX = RMSD x Number of residues in the larger domain/number of aligned residues).

What is a Distant Structural Cluster?

A Distant Structural Cluster describes a cluster of two or CATH domains that have been grouped together with a more relaxed structural similarity threshold to investigate more distant evolutionary similarities (SIMAX score < 5Å where SIMAX = RMSD x Number of residues in the larger domain/number of aligned residues).

What is a Structural Neighbour?

The term "structural neighbour" is used here to describe two CATH domains that share a degree of structural similarity. The SSAP algorithm is used to calculate this similarity and works by generating a structure-based pairwise alignment of the two domains then scoring this alignment using a RMSD score which has been normalised by the length of the larger domain divided by the number of aligned residues (SIMAX).

S100 Family: 3.10.28.10.9.1.1.1

Classification Lineage (3.10.28.10.9.1.1.1)

Summary of Non-Redundant Representatives

What is a Non-Redundant Representative?

S100 Count Entries in S100 Family 3.10.28.10.9.1.1.1 (8)

What is a Non-Redundant Representative?

Why can't I have a multiple structural alignment of the whole superfamily?

What is an Close Structural Cluster?

What is a Distant Structural Cluster?

What is a Structural Neighbour?

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