Structural Classification of Proteins
Fold: Ribonuclease H-like motif
3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145; strand 2 is antiparallel to the rest
Lineage:
Root:
scop
Class:
Alpha and beta proteins (a/b)
[51349]
Mainly parallel beta sheets (beta-alpha-beta units)
Fold:
Ribonuclease H-like motif
[53066]
3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145; strand 2 is antiparallel to the rest
Superfamilies:
Actin-like ATPase domain
[53067] (14)
duplication contains two domains of this fold
uperfamily
Actin/HSP70
[53068] (14)
Heat shock protein 70kDa, ATPase fragment [53069]
Cow (Bos taurus)
[TaxId: 9913]
[53070] (51)
Human (Homo sapiens)
[TaxId: 9606]
[53071] (14)
Escherichia coli, gene dnaK
[TaxId: 562]
[53072] (1)
Actin [53073]
Cow (Bos taurus)
[TaxId: 9913]
[53074] (68)
Rabbit (Oryctolagus cuniculus)
[TaxId: 9986]
[53075] (20)
SQ
P02568
! SQ 02568
Chicken (Gallus gallus)
[TaxId: 9031]
[82437] (1)
sequence identical to the rabbit actin
Nematode (Caenorhabditis elegans)
[TaxId: 6239]
[64086] (1)
Dictyostelium discoideum
[TaxId: 44689]
[53076] (6)
Baker's yeast (Saccharomyces cerevisiae)
[TaxId: 4932]
[53077] (2)
Prokaryotic actin homolog MreB [64087]
Thermotoga maritima
[TaxId: 2336]
[64088] (3)
Actin-related protein 3, Arp3 [69528]
part of Arp2/3 complex
Cow (Bos taurus)
[TaxId: 9913]
[69529] (17)
SQ
P61158
Actin-related protein 2, Arp2 [69530]
part of Arp2/3 complex
Cow (Bos taurus)
[TaxId: 9913]
[69531] (3)
SQ
P61160
143-350 # 100% sequence identity
Cell division protein FtsA [53078]
Thermotoga maritima
[TaxId: 2336]
[53079] (2)
Plasmid segregation protein ParM [82438]
Escherichia coli
[TaxId: 562]
[82439] (14)
BadF/BadG/BcrA/BcrD-like
[64089] (5)
Hydroxyglutaryl-CoA dehydratase component A [64090]
Acidaminococcus fermentans
[TaxId: 905]
[64091] (1)
Hypothetical protein PG1100 [142452]
Porphyromonas gingivalis
[TaxId: 837]
[142453] (2)
SQ
Q7MVG4
1-107! SQ
Q7MVG4
108-283
Probable N-acetylglucosamine kinase CV2896 [142454]
Chromobacterium violaceum
[TaxId: 536]
[142455] (4)
SQ
Q7NU07
122-292! SQ
Q7NU07
8-121
Hypothetical protein BT3618 [142456]
Bacteroides thetaiotaomicron
[TaxId: 818]
[142457] (12)
SQ
Q8A1P1
107-280! SQ
Q8A1P1
3-106
N-acetylglucosamine kinase, NAGK [142458]
Human (Homo sapiens)
[TaxId: 9606]
[142459] (16)
SQ
Q9UJ70
1-117! SQ
Q9UJ70
118-344
Acetokinase-like
[53080] (3)
Acetate kinase [53081]
Archaeon Methanosarcina thermophila
[TaxId: 2210]
[53082] (6)
SQ
P38502
1-399
butyrate kinase 2 [142460]
Thermotoga maritima
[TaxId: 2336]
[142461] (18)
SQ
Q9X278
1-172! SQ
Q9X278
173-375
Propionate kinase [142462]
Salmonella typhimurium
[TaxId: 90371]
[142463] (10)
SQ
O06961
193-397! SQ
O06961
4-192
ATPase domain of dehydratase reactivase alpha subunit
[82440] (2)
ATPase domain of the glycerol dehydratase reactivase alpha subunit [82441]
includes the insert and linker domains
Klebsiella pneumoniae
[TaxId: 573]
[82442] (1)
Diol dehydratase-reactivating factor large subunit DdrA [142464]
Klebsiella oxytoca
[TaxId: 571]
[142465] (8)
SQ
O68195
1-92,255-403! SQ
O68195
404-606
Hexokinase
[53083] (5)
Hexokinase [53084]
Baker's yeast (Saccharomyces cerevisiae), pII
[TaxId: 4932]
[64092] (1)
Blood fluke (Schistosoma mansoni)
[TaxId: 6183]
[53085] (1)
Glucokinase [102479]
Hexokinase D
Human (Homo sapiens)
[TaxId: 9606]
[102480] (2)
Mammalian type I hexokinase [53086]
further duplication: consists of two very similar lobes
Human (Homo sapiens)
[TaxId: 9606]
[53087] (5)
Rat (Rattus norvegicus)
[TaxId: 10116]
[53088] (1)
Glycerol kinase
[53089] (2)
Glycerol kinase [53090]
Escherichia coli
[TaxId: 562]
[53091] (28)
Enterococcus casseliflavus
[TaxId: 37734]
[117641] (2)
SQ
O34153
5-491
Glucokinase
[110627] (1)
Pfam 02685
Glucokinase Glk [110628]
Escherichia coli
[TaxId: 562]
[110629] (2)
SQ
P46880
P0A6V8
Ppx/GppA phosphatase
[110630] (2)
Pfam 02541
Exopolyphosphatase Ppx [110631]
Aquifex aeolicus
[TaxId: 63363]
[110632] (6)
SQ
O67040
Escherichia coli
[TaxId: 562]
[142466] (12)
SQ
P0AFL6
11-134! SQ
P0AFL6
135-311
YeaZ-like
[110633] (2)
Pfam 00814
; ubiquitous cytoplasmic protein; annotated as Glycoprotease (Peptidase_M22 family) on the basis of one member's known extracellular activity
Hypothetical protein YeaZ [110634]
Escherichia coli
[TaxId: 562]
[110635] (1)
SQ
P76256
Hypothetical protein TM0874 [142467]
Thermotoga maritima
[TaxId: 2336]
[142468] (4)
SQ
Q9WZX7
1-103! SQ
Q9WZX7
104-193
ROK
[110636] (8)
Pfam 00480
Inorganic polyphosphate/ATP-glucomannokinase PPGMK [110637]
Arthrobacter sp. KM
[TaxId: 184230]
[110638] (1)
SQ
Q7WT42
11-263 # Fragment
Putative fructokinase YhdR [117642]
Bacillus subtilis
[TaxId: 1423]
[117643] (1)
SQ
O05510
N-acetylglucosamine kinase [142469]
Transcriptional regulator, XylR-related
Thermotoga maritima
[TaxId: 2336]
[142470] (2)
SQ
Q9X0V1
200-368! SQ
Q9X0V1
72-199
TM1224
N-acetylmannosamine kinase NanK [142471]
Escherichia coli
[TaxId: 562]
[142472] (4)
SQ
P45425
1-119! SQ
P45425
120-289
Mlc protein [142473]
Making large colonies protein
Escherichia coli
[TaxId: 562]
[142474] (12)
SQ
P50456
211-406! SQ
P50456
82-210
Putative regulator protein YcfX [142475]
Salmonella typhimurium
[TaxId: 90371]
[142476] (2)
SQ
Q8ZPZ9
1-117! SQ
Q8ZPZ9
118-303
Hypothetical protein SP2142 [142477]
Streptococcus pneumoniae
[TaxId: 1313]
[142478] (2)
SQ
Q97NB0
1-114! SQ
Q97NB0
115-289
Transcriptional regulator VC2007 [142479]
Vibrio cholerae
[TaxId: 666]
[142480] (2)
SQ
Q9KQJ1
209-405! SQ
Q9KQJ1
81-208
Cyto-EpsL domain
[117644] (1)
N-terminal part of
Pfam 05134
Cytoplasmic domain of general secretion pathway protein L, EpsL [117645]
Vibrio cholerae
[TaxId: 666]
[117646] (7)
SQ
P45782
6-244
Ta0583-like
[142481] (1)
Hypothetical protein Ta0583 [142482]
Archaeon Thermoplasma acidophilum
[TaxId: 2303]
[142483] (10)
SQ
Q9HKL4
1-164! SQ
Q9HKL4
165-325
CoaX-like
[142484] (3)
Pfam 03309
; Bordetella pertussis Bvg accessory factor family, Baf
Type III pantothenate kinase, CoaX [142485]
Thermotoga maritima
[TaxId: 2336]
[142486] (48)
SQ
Q9WZY5
1-118! SQ
Q9WZY5
119-245
Pseudomonas aeruginosa
[TaxId: 287]
[142487] (8)
SQ
Q9HWC1
1-114! SQ
Q9HWC1
115-248
Campylobacter jejuni
[TaxId: 197]
[142488] (4)
SQ
Q5HW73
1-82! SQ
Q5HW73
83-208
Fumble-like
[159623] (3)
Pfam 03630
; type II pantothenate kinase-like
Pantothenate kinase 3, PANK3 [159624]
Human (Homo sapiens)
[TaxId: 9606]
[159625] (8)
SQ
Q9H999
12-152! SQ
Q9H999
157-368
Type II pantothenate kinase, CoaW [159626]
Staphylococcus aureus
[TaxId: 1280]
[159627] (2)
SQ
Q8NVG0
1-267
Pantothenate kinase 1, PANK1 [159628]
Human (Homo sapiens)
[TaxId: 9606]
[159629] (4)
SQ
Q8TE04
236-381! SQ
Q8TE04
382-593
Creatinase/prolidase N-terminal domain
[53092] (1)
uperfamily
Creatinase/prolidase N-terminal domain
[53093] (4)
Creatinase [53094]
Pseudomonas putida
[TaxId: 303]
[53095] (1)
Actinobacillus sp.
[TaxId: 41114]
[75244] (1)
Aminopeptidase P [53096]
synonym: Xaa-Pro dipeptidase, prolidase
Escherichia coli
[TaxId: 562]
[53097] (37)
Archaeon Pyrococcus furiosus
[TaxId: 2261]
[102481] (1)
Ribonuclease H-like
[53098] (14)
consists of one domain of this fold
uperfamily
Ribonuclease H
[53099] (11)
RNase H (RNase HI) [53100]
Escherichia coli
[TaxId: 562]
[53101] (37)
SQ
P0A7Y4
Thermus thermophilus
[TaxId: 274]
[53102] (1)
synthetic, Escherichia coli/Thermus thermophilus chimera
[69532] (1)
Class II ribonuclease H (RNase HII) [53103]
Archaeon Methanococcus jannaschii
[TaxId: 2190]
[53104] (1)
Archaeon Archaeoglobus fulgidus
[TaxId: 2234]
[64093] (2)
Archaeon Thermococcus kodakaraensis
[TaxId: 311400]
[64094] (2)
Archaeon Pyrococcus horikoshii
[TaxId: 53953]
[110639] (2)
SQ
O59351
Thermotoga maritima
[TaxId: 2336]
[142489] (1)
SQ
Q9X017
1-221
HIV RNase H (Domain of reverse transcriptase) [53105]
Human immunodeficiency virus type 1
[TaxId: 11676]
[53106] (88)
SQ
P04585
159-692 # chain A coverage; chain B is shorter: 162-582 ! SQ
P03366
186-725 # chain A coverage; chain B coverage: 156-584 ! SQ
P04585
158-698 # chain A coverage; chain B is shorter: 159-595
Human immunodeficiency virus type 2
[TaxId: 11709]
[82443] (1)
BH0863-like Ribonuclease H [142490]
new class of RNase H
Bacillus halodurans
[TaxId: 86665]
[142491] (15)
SQ
Q9KEI9
61-193! SQ
Q9KEI9
62-193
BH0863
Retroviral integrase, catalytic domain
[53107] (3)
Retroviral integrase, catalytic domain [53108]
Rous sarcoma virus RSV
[TaxId: 11886]
[53109] (21)
Human immunodeficiency virus type 1
[TaxId: 11676]
[53110] (19)
Simian immunodeficiency virus
[TaxId: 11723]
[53111] (1)
mu transposase, core domain
[53112] (1)
mu transposase, core domain [53113]
Bacteriophage mu
[TaxId: 10677]
[53114] (2)
Transposase inhibitor (Tn5 transposase)
[53115] (1)
Transposase inhibitor (Tn5 transposase) [53116]
contains additional all-alpha subdomains in both N- and C-terminal regions
Escherichia coli
[TaxId: 562]
[53117] (6)
DnaQ-like 3'-5' exonuclease
[53118] (26)
contains
Pfam 00929
Exonuclease domain of prokaryotic DNA polymerase [53119]
part of Klenow fragment, KF
Escherichia coli
[TaxId: 562]
[53120] (14)
Thermus aquaticus
[TaxId: 271]
[53121] (13)
Bacillus stearothermophilus, newly identified strain as yet unnamed
[TaxId: 1422]
[53122] (45)
SQ
Q45458
298-876 # 88% sequence identity ! SQ
Q5KWC1
299-878 # 99% sequence identity; Geobacillus kaustophilus TaxID:1462
Exonuclease domain of T7 DNA polymerase [53123]
Bacteriophage T7
[TaxId: 10760]
[53124] (16)
SQ
P00581
Exonuclease domain of family B DNA polymerases [53125]
elaborated with additional structures and the N-terminal subdomain
Escherichia coli
[TaxId: 562]
[102482] (1)
DNA polymerase II, additional N-terminal subdomain has an OB-fold with a ferredoxin-like fold insertion
Bacteriophage T4
[TaxId: 10665]
[53126] (2)
additional N-terminal subdomain contains rudimental OB-fold
Bacteriophage RB69
[TaxId: 12353]
[53127] (27)
additional N-terminal subdomain contains rudimental OB-fold and rudimental ferredoxin-like fold
Archaeon Thermococcus gorgonarius
[TaxId: 71997]
[53128] (3)
additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold
Archaeon Thermococcus sp., 9on-7
[TaxId: 35749]
[53129] (1)
additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold
Archaeon Desulfurococcus tok
[TaxId: 108142]
[53130] (2)
additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold
Archaeon Pyrococcus kodakaraensis
[TaxId: 311400]
[53131] (2)
SQ
P56689
1-758 # 93% sequence identity; Thermococcus kodakarensis KOD1 TaxID: 69014
additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold
Sulfolobus solfataricus
[TaxId: 2287]
[117647] (1)
SQ
P26811
40-864
N-terminal exonuclease domain of the epsilon subunit of DNA polymerase III [82444]
Escherichia coli
[TaxId: 562]
[82445] (5)
Exonuclease I [53132]
also includes an alpha+beta domain with SH3-like like motif and non-globular C-terminal all-alpha region
Escherichia coli
[TaxId: 562]
[53133] (1)
Escherichia coli K12 (Escherichia coli K-12)
[TaxId: 83333]
[159630] (3)
Oligoribonuclease [89719]
Haemophilus influenzae
[TaxId: 727]
[89720] (1)
HI1715
Escherichia coli
[TaxId: 562]
[142492] (6)
SQ
P0A784
1-180
Hypothetical protein AT5G06450 [102483]
forms a ring-shaped hexamer; function unknown
Thale-cress (Arabidopsis thaliana)
[TaxId: 3702]
[102484] (7)
Exonuclease ERI1 [117648]
Human (Homo sapiens)
[TaxId: 9606]
[117649] (1)
SQ
Q8IV48
122-321
Exonuclease domain of phi29 DNA polymerase [117650]
Bacteriophage phi-29
[TaxId: 10756]
[117651] (18)
SQ
P03680
Interferon-stimulated gene 20 kDa protein, ISG20 [117652]
Human (Homo sapiens)
[TaxId: 9606]
[117653] (1)
SQ
Q96AZ6
6-178
Exosome complex exonuclease RRP6 [142493]
Baker's yeast (Saccharomyces cerevisiae)
[TaxId: 4932]
[142494] (4)
SQ
Q12149
129-420
Ribonuclease D, catalytic domain [142495]
Escherichia coli
[TaxId: 562]
[142496] (1)
SQ
P09155
1-193
Ribonuclease T [142497]
Pseudomonas aeruginosa
[TaxId: 287]
[142498] (2)
SQ
Q9HY82
19-220
Three prime repair exonuclease 2, TREX2 [142499]
Human (Homo sapiens)
[TaxId: 9606]
[142500] (2)
SQ
Q9BQ50
44-271
Three prime repair exonuclease 1, TREX1 [159631]
Mouse (Mus musculus)
[TaxId: 10090]
[159632] (18)
SQ
Q91XB0
5-234! SQ
Q91XB0
9-234
RuvC resolvase
[53134] (1)
RuvC resolvase [53135]
Holliday junction-specific endonuclease
Escherichia coli
[TaxId: 562]
[53136] (1)
Mitochondrial resolvase ydc2 catalytic domain
[69533] (1)
Mitochondrial resolvase ydc2 catalytic domain [69534]
Fission yeast (Schizosaccharomyces pombe)
[TaxId: 4896]
[69535] (1)
Putative Holliday junction resolvase RuvX
[102485] (3)
Hypothetical protein YqgF (RuvX) [102486]
Escherichia coli
[TaxId: 562]
[102487] (3)
Hypothetical protein YrrK (RuvX) [102488]
Bacillus subtilis
[TaxId: 1423]
[102489] (1)
Hypothetical protein, YqgF homologue [102490]
Thermus thermophilus
[TaxId: 274]
[102491] (1)
CAF1-like ribonuclease
[102492] (2)
Pop2 RNase D domain [102493]
Baker's yeast (Saccharomyces cerevisiae)
[TaxId: 4932]
[102494] (1)
CCR4-NOT transcription complex subunit 7, CAF1 [159633]
Human (Homo sapiens)
[TaxId: 9606]
[159634] (1)
SQ
Q9UIV1
11-262
PIWI domain
[110640] (3)
Pfam 02171
Argonaute homologue PF0537 [110641]
includes the middle domain
Pyrococcus furiosus
[TaxId: 2261]
[110642] (3)
SQ
Q8U3D2
Argonaute homologue Aq_1447 [142501]
includes the middle domain
Aquifex aeolicus
[TaxId: 63363]
[142502] (6)
SQ
O67434
315-706
Hypothetical protein AF1318 [142503]
Archaeoglobus fulgidus
[TaxId: 2234]
[142504] (5)
SQ
O28951
11-427
TM1739-like
[142505] (1)
Pfam 04251
; DUF430; particular similarity to the PIWI domain family
Hypothetical protein TM1739 [142506]
Thermotoga maritima
[TaxId: 2336]
[142507] (2)
SQ
Q9X261
1-301
Hermes transposase-like
[142508] (1)
Transposase Hermes, catalytic domain [142509]
House fly (Musca domestica)
[TaxId: 7370]
[142510] (1)
SQ
Q25442
163-609
Tex RuvX-like domain-like
[159635] (1)
Transcriptional accessory factor Tex [159636]
Pseudomonas aeruginosa
[TaxId: 287]
[159637] (3)
SQ
Q9HTY8
325-473
Prp8 beta-finger domain-like
[159638] (2)
Pre-mRNA-splicing factor 8, Prp8 [159639]
Human (Homo sapiens)
[TaxId: 9606]
[159640] (3)
SQ
Q6P2Q9
1760-2016! SQ
Q6P2Q9
1771-1989
Saccharomyces cerevisiae
[TaxId: 4932]
[159641] (5)
SQ
P33334
1833-2087! SQ
P33334
1835-2087
Translational machinery components
[53137] (2)
uperfamily
Ribosomal protein L18 and S11
[53138] (7)
Ribosomal protein L18 (L18p) [53139]
Archaeon Haloarcula marismortui
[TaxId: 2238]
[53140] (40)
SQ
P14123
Thermus thermophilus
[TaxId: 274]
[75245] (7)
Bacillus stearothermophilus
[TaxId: 1422]
[102495] (1)
Escherichia coli
[TaxId: 562]
[159642] (29)
SQ
P0C018
1-117
Deinococcus radiodurans
[TaxId: 1299]
[159643] (6)
SQ
Q9RSL2
8-111
Ribosomal protein S11 [53141]
Thermus thermophilus
[TaxId: 274]
[53142] (46)
SQ
P80376
Escherichia coli
[TaxId: 562]
[159644] (24)
SQ
P0A7R9
12-128
ERF1/Dom34 middle domain-like
[53143] (3)
Middle domain of eukaryotic peptide chain release factor subunit 1, ERF1 [53144]
Human (Homo sapiens)
[TaxId: 9606]
[53145] (2)
Dom34 [159645]
Saccharomyces cerevisiae
[TaxId: 4932]
[159646] (3)
SQ
P33309
136-277
Cell division protein pelota [159647]
Thermoplasma acidophilum
[TaxId: 2303]
[159648] (1)
SQ
Q9HJ74
127-243
Nitrogenase accessory factor-like
[53146] (2)
uperfamily
MTH1175-like
[53147] (3)
Hypothetical protein MTH1175 [53148]
Archaeon Methanobacterium thermoautotrophicum
[TaxId: 145262]
[53149] (1)
Hypothetical protein TM1816 [82446]
Thermotoga maritima
[TaxId: 2336]
[82447] (2)
SQ
Q9X2D6
1-115
Hypothetical protein TM1290 [110643]
Thermotoga maritima
[TaxId: 2336]
[110644] (1)
SQ
Q9X116
Nitrogenase accessory factor
[102496] (1)
capable of binding the iron molybdenum cofactor, FeMo-co
NafY core domain [102497]
Azotobacter vinelandii
[TaxId: 354]
[102498] (1)
DNA repair protein MutS, domain II
[53150] (1)
uperfamily
DNA repair protein MutS, domain II
[53151] (2)
DNA repair protein MutS, domain II [53152]
Thermus aquaticus
[TaxId: 271]
[53153] (4)
Escherichia coli
[TaxId: 562]
[53154] (10)
SQ
P23909
2-800
Methylated DNA-protein cysteine methyltransferase domain
[53155] (1)
uperfamily
Methylated DNA-protein cysteine methyltransferase domain
[53156] (3)
Ada DNA repair protein [53157]
Escherichia coli
[TaxId: 562]
[53158] (1)
O6-alkylguanine-DNA alkyltransferase [53159]
Human (Homo sapiens)
[TaxId: 9606]
[53160] (9)
SQ
P16455
6-176
Archaeon Pyrococcus kodakaraensis
[TaxId: 311400]
[53161] (1)
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key:
Generated from scop database 1.75 with scopm 1.101 on Wed Jun 3 10:42:06 2009
Copyright
© 1994-2009 The scop authors / scop@mrc-lmb.cam.ac.uk