Architecture: 3.10

Representative domain: 3dlkB01

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Classification Lineage (3.10)

CATH Code	Level Description	Links
3	Alpha Beta
3.10	Roll

Summary of Non-Redundant Representatives


-	-	58	100	501	675	902	1766	6522

Non-Redundant Representatives (58)
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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).

Topology Entries in Architecture 3.10 (58)

CATH code	Name	Representative Domain	Representative Keywords	Number of Domains
3.10.10	HIV Type 1 Reverse Transcriptase; Chain A, domain 1	3dlkB01	DNA-directed DNA polymerase.Human immunodeficiency virus type 1 BH10Retroviral ribonuclease H.HIV-1 retropepsin.Gag-Pol polyprotein	319
3.10.20	Ubiquitin-like (UB roll)	1igdA00	Streptococcus sp. 'group G'Immunoglobulin G-binding protein G	1291
3.10.25	Methionyl-tRNA Fmet Formyltransferase; Chain A, domain 2	2bw0A02	10-formyltetrahydrofolate catabolic processOne carbon pool by folate10-formyltetrahydrofolate dehydrogenaseFormyltetrahydrofolate dehydrogenase [EC:1.5.1.6]Formyltetrahydrofolate dehydrogenase.	7
3.10.28	Endonuclease I-creI	2ab5A02	Cytochrome b mRNA maturase bI3Oxidative phosphorylationGroup I intron splicingRNA bindingUbiquinol-cytochrome c reductase cytochrome b subunit [EC:1.10.2.2]	119
3.10.40	Pertussis Toxin; Chain B, domain 1	3g4nA01	AerolysinAeromonas hydrophila	26
3.10.50	Chitinase A; domain 3	1itxA02	Chitinase.Bacillus circulansChitinase A1	354
3.10.100	Mannose-Binding Protein A; Chain A	2zibA00	Brachyopsis rostratusType II antifreeze protein	438
3.10.105	Dipeptide-binding Protein; domain 3	1jetA03	Salmonella enterica subsp. enterica serovar TyphimuriumPeptide/nickel transport system substrate-binding proteinABC transportersPeriplasmic oligopeptide-binding protein	40
3.10.110	Ubiquitin Conjugating Enzyme	1z2uA00	Caenorhabditis elegansLocomotionHermaphrodite genitalia developmentDetermination of adult lifespanUbiquitin-conjugating enzyme E2 2	135
3.10.120	Flavocytochrome B2; Chain A, domain 1	1cyoA00	Bos taurusCytochrome b5	79
3.10.129	Thiol Ester Dehydrase; Chain A	1vh5A00	Esterase ydiIEscherichia coli K-12Acting on ester bonds.	389
3.10.130	P-30 Protein	1dy5A00	Bos taurusPancreatic ribonuclease [EC:3.1.27.5]Pancreatic ribonuclease.Ribonuclease pancreaticProtein binding	417
3.10.150	DNA Polymerase III; Chain A, domain 2	3d1gA01	Pyrimidine metabolismDNA replicationPurine metabolismDNA polymerase III subunit betaProtein binding	67
3.10.170	Elastase; domain 1	1u4gA01	Pseudomonas aeruginosaPseudolysinPseudolysin.Pseudolysin [EC:3.4.24.26]	71
3.10.180	2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1	1nkiA00	Pseudomonas aeruginosaGlutathione transferase fosAGlutathione transferase.	374
3.10.196	Cobalamin-dependent Methionine Synthase; domain 1	2o2kA01	Nervous system developmentOne carbon pool by folateProtein bindingMetabolic pathways5-methyltetrahydrofolate--homocysteine methyltransferase [EC:2.1.1.13]	8
3.10.200	Carbonic Anhydrase II	3ks3A00	Nitrogen metabolismZinc ion bindingNucleusCarbonic anhydrase [EC:4.2.1.1]Proximal tubule bicarbonate reclamation	373
3.10.250	Mac-2 Binding Protein	1z8gA01	Serine protease hepsinIntegral to plasma membraneHepsin (transmembrane protease, serine 1) [EC:3.4.21.-]Homo sapiensHepsin.	8
3.10.260	Mlu1-box Binding Protein; DNA-binding Domain	1bm8A00	DNA replicationPositive regulation of gene-specific transcriptionTranscription factor MBP1Protein bindingSequence-specific DNA binding transcription factor activity	18
3.10.270	Urate Oxidase	3l8wA00	Urate oxidase [EC:1.7.3.3]Purine metabolismAspergillus flavusFactor independent urate hydroxylase.Uricase	109
3.10.280	Mitochondrial Matrix Protein; Chain A	1p32C00	Complement component 1 Q subcomponent-binding protein, mitochondrialPlasma membraneImmune responseHomo sapiens	3
3.10.290	Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A	1dm9A00	Ribosomal large subunit bindingHeat shock protein 15Protein bindingEscherichia coli K-12Cellular response to heat	121
3.10.300	3-methyladenine DNA Glycosylase; Chain A	1ewnA00	DNA dealkylation involved in DNA repairDNA-3-methyladenine glycosylaseIdentical protein bindingDNA-3-methyladenine glycosylase II.Homo sapiens	4
3.10.310	Diaminopimelate Epimerase; Chain A, domain 1	1xubA02	Phenazine biosynthesis protein phzFPseudomonas fluorescensRacemases and epimerases.	64
3.10.320	Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1	1iakB01	Antigen processing and presentation of exogenous peptide antigen via MHC class IIMultivesicular bodyH-2 class II histocompatibility antigen, A-K beta chainPeptide antigen bindingIntegral to membrane	236
3.10.330	Vcp-like ATPase; Chain A, domain 2	1wlfA02	Mus musculusPeroxisome biogenesis factor 1	28
3.10.340	Methenyltetrahydromethanopterin Cyclohydrolase; Chain A, domain 1	1qlmA01	Methanopyrus kandleriMethenyltetrahydromethanopterin cyclohydrolase.Methenyltetrahydromethanopterin cyclohydrolase	1
3.10.350	Membrane-bound Lytic Murein Transglycosylase D; Chain A	1y7mA01	Bacillus subtilisPutative L,D-transpeptidase YkuDTransferases.	4
3.10.360	Antimicrobial Peptide, Beta-defensin 2; Chain A	1fd3A00	Homo sapiensImmune responseBeta-defensin 2G-protein coupled receptor protein signaling pathwayChemotaxis	22
3.10.370	Transcription Factor TfIIh p44 Subunit; Chain A	1z60A00	Nucleotide excision repairProtein N-terminus bindingBasal transcription factorsG-protein coupled receptor internalizationHolo TFIIH complex	2
3.10.380	Ribonuclease domain of colicin e3 (Residues 456-551)	2b5uA03	Colicin-E3Escherichia coliActing on ester bonds.	6
3.10.390	SAND domain	1oqjA00	Glucocorticoid modulatory element-binding protein 1NucleusHomo sapiensTranscription coactivator activity	6
3.10.400	Sulfate adenylyltransferase	1r6xA01	Identical protein bindingSelenoamino acid metabolismSulfur metabolismPurine metabolismSulfate adenylyltransferase (ATP) activity	23
3.10.410	Formyltetrahydrofolate synthetase; domain 3	1eg7A03	Formate--tetrahydrofolate ligaseMoorella thermoaceticaFormate--tetrahydrofolate ligase.	6
3.10.420	Bacterial Protein-export protein SecB	2hngA00	Streptococcus pneumoniaePutative uncharacterized protein	21
3.10.430	Ribosomal Protein L9; domain 2	1divA02	Geobacillus stearothermophilus50S ribosomal protein L9	38
3.10.440	Ribosomal Protein L31e; Chain: W;	1vq8X00	Large subunit ribosomal protein L31eRibosome50S ribosomal protein L31eHaloarcula marismortui	64
3.10.450	Nuclear Transport Factor 2; Chain: A,	2o9uX00	Monellin chain BDioscoreophyllum cumminsii	1139
3.10.460	VSV matrix protein	1lg7A00	Matrix proteinVesicular stomatitis Indiana virus (strain 94GUB Central America)	1
3.10.470	chromosomal protein mc1	1t23A00	Chromosomal protein MC1Methanosarcina thermophila	2
3.10.480	Protein pf0470	2z0tA00	Putative uncharacterized protein PH0355Pyrococcus horikoshii	6
3.10.490	Hypothetical upf0131 protein ytfp	3judA00	AIG2-like domain-containing protein 1Homo sapiens	19
3.10.500	prostaphopain b, domain 1	1x9yA01	Cysteine endopeptidases.Staphopain BStaphylococcus aureus	4
3.10.510	NE1680-like fold	2hfqA00	Nitrosomonas europaeaPutative uncharacterized protein	1
3.10.520	T-fold	2o34A00	Hypothetical proteinDesulfovibrio vulgaris str. HildenboroughPutative uncharacterized protein	2
3.10.530	CPE0013-like fold	2jovA01	Putative uncharacterized protein CPE0013Clostridium perfringens	1
3.10.540	duf1285 like fold	2ra9A01	Hypothetical proteinShewanella baltica OS155Putative uncharacterized protein	3
3.10.550	Atu2299-like	2hlyA00	Agrobacterium tumefaciens str. C58Putative uncharacterized protein	1
3.10.560	Outer membrane lipoprotein wza fold like	2j58A01	Putative outer membrane lipoprotein WzaEscherichia coli	16
3.10.570	sex pheromone staph- cam373 precursor fold	2qx2A00	Sex pheromone staph-cAM373Staphylococcus aureus subsp. aureus Mu50	1
3.10.580	CBS-domain	3gbyA00	Chlorobaculum tepidumPutative uncharacterized protein	11
3.10.590	ph1033 like fold	2hd9A00	Pyrococcus horikoshiiUPF0310 protein PH1033	4
3.10.600	pyruvate carboxylase f1077a mutant fold	2qf7A03	Pyruvate carboxylase subunit A [EC:6.4.1.1]Pyruvate carboxylase.Citrate cycle (TCA cycle)Rhizobium etli CFN 42Pyruvate carboxylase subunit B [EC:6.4.1.1]	8
3.10.610	Pili subunits	3ci0J01	General secretion pathway protein JHypothetical type II secretion proteinBacterial secretion systemEscherichia coli	1
3.10.620	C8orf32 fold	3c9qA00	Homo sapiensProtein N-terminal glutamine amidohydrolaseProtein bindingIn linear amides.	1
3.10.630	dip2346 fold like	3bh1A01	UPF0371 protein DIP2346Corynebacterium diphtheriae	4
3.10.640	Restriction endonuclease-like alpha-beta roll fold	2g3wA00	Xanthomonas axonopodis pv. citriPutative uncharacterized protein	5
3.10.650	MalF N-terminal region-like	2r6gF02	Maltose-transporting ATPase activityMaltooligosaccharide-importing ATPase activityMaltose transport system permease protein malFATP-binding cassette (ABC) transporter complexMaltose transport	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).

Architecture: 3.10

Roll

Classification Lineage (3.10)

Summary of Non-Redundant Representatives

What is a Non-Redundant Representative?

Topology Entries in Architecture 3.10 (58)

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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