S100 Family: 2.40.50.140.9.1.1.3

Representative domain: 2pi2E00

Classification Lineage (2.40.50.140.9.1.1.3)

CATH Code	Level Description	Links
2	Mainly Beta
2.40	Beta Barrel
2.40.50	OB fold (Dihydrolipoamide Acetyltransferase, E2P)
2.40.50.140	Nucleic acid-binding proteins	Gene3D
2.40.50.140.9
2.40.50.140.9.1
2.40.50.140.9.1.1
2.40.50.140.9.1.1.3

Summary of Non-Redundant Representatives


-	-	-	-	-	-	-	-	12

Non-Redundant Representatives (12)
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 2.40.50.140.9.1.1.3 (12)

CATH code	Domain ID	Keywords
2.40.50.140.9.1.1.3.1	2pi2E00	Replication protein A 14 kDa subunit, single-stranded DNA binding, Homo sapiens, Homologous recombination, replication factor A3, Nucleotide excision repair, DNA replication factor A complex, cytoplasm, DNA replication, Mismatch repair
2.40.50.140.9.1.1.3.2	2pi2H00	Nucleotide excision repair, DNA replication factor A complex, Homologous recombination, Homo sapiens, replication factor A3, single-stranded DNA binding, Replication protein A 14 kDa subunit, Mismatch repair, DNA replication, cytoplasm
2.40.50.140.9.1.1.3.3	2pi2G00	Mismatch repair, cytoplasm, DNA replication, Homologous recombination, Homo sapiens, replication factor A3, Nucleotide excision repair, DNA replication factor A complex, Replication protein A 14 kDa subunit, single-stranded DNA binding
2.40.50.140.9.1.1.3.4	2pi2F00	Nucleotide excision repair, DNA replication factor A complex, Homologous recombination, Homo sapiens, replication factor A3, single-stranded DNA binding, Replication protein A 14 kDa subunit, Mismatch repair, DNA replication, cytoplasm
2.40.50.140.9.1.1.3.5	1quqB00	DNA replication, cytoplasm, Mismatch repair, single-stranded DNA binding, Replication protein A 14 kDa subunit, DNA replication factor A complex, Nucleotide excision repair, replication factor A3, Homologous recombination, Homo sapiens
2.40.50.140.9.1.1.3.6	2pqaB00	Mismatch repair, cytoplasm, DNA replication, Homo sapiens, Homologous recombination, replication factor A3, Nucleotide excision repair, DNA replication factor A complex, Replication protein A 14 kDa subunit, single-stranded DNA binding
2.40.50.140.9.1.1.3.7	2pqaD00	Mismatch repair, cytoplasm, DNA replication, replication factor A3, Homo sapiens, Homologous recombination, DNA replication factor A complex, Nucleotide excision repair, Replication protein A 14 kDa subunit, single-stranded DNA binding
2.40.50.140.9.1.1.3.8	1quqD00	Homo sapiens, Homologous recombination, replication factor A3, Nucleotide excision repair, DNA replication factor A complex, Replication protein A 14 kDa subunit, single-stranded DNA binding, Mismatch repair, cytoplasm, DNA replication
2.40.50.140.9.1.1.3.9	1l1oA00	Nucleotide excision repair, DNA replication factor A complex, Homo sapiens, Homologous recombination, replication factor A3, single-stranded DNA binding, Replication protein A 14 kDa subunit, Mismatch repair, DNA replication, cytoplasm
2.40.50.140.9.1.1.3.10	1l1oD00	Mismatch repair, DNA replication, cytoplasm, Nucleotide excision repair, DNA replication factor A complex, Homo sapiens, Homologous recombination, replication factor A3, single-stranded DNA binding, Replication protein A 14 kDa subunit
2.40.50.140.9.1.1.3.11	2z6kC00	Homologous recombination, Homo sapiens, replication factor A3, Nucleotide excision repair, DNA replication factor A complex, Replication protein A 14 kDa subunit, single-stranded DNA binding, Mismatch repair, cytoplasm, DNA replication
2.40.50.140.9.1.1.3.12	2z6kD00	single-stranded DNA binding, Replication protein A 14 kDa subunit, Nucleotide excision repair, DNA replication factor A complex, Homologous recombination, Homo sapiens, replication factor A3, DNA replication, cytoplasm, Mismatch repair

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=2.40.50.140.9.1.1.3

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: 2.40.50.140.9.1.1.3

Classification Lineage (2.40.50.140.9.1.1.3)

Summary of Non-Redundant Representatives

What is a Non-Redundant Representative?

S100 Count Entries in S100 Family 2.40.50.140.9.1.1.3 (12)

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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