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UniProtKB - P54602 (YHCR_BACSU)
Protein
Endonuclease YhcR
Gene
yhcR
Organism
Bacillus subtilis (strain 168)
Status
Functioni
Sugar-nonspecific endonuclease that yields nucleotide 3'-monophosphate products. No 5'-nucleotidase activity was detected, using 5'-AMP as the substrate, in the presence of diverse divalent metals and with various pH values.
1 PublicationCofactori
Activity regulationi
Requires a minimum of 0.1 mM of calcium for a significant activity. Maximal activity was observed with concentrations of calcium between 1 to 5 mM. Is 10-fold less active with the corresponding concentrations of manganese. Inhibited by NaCl at concentrations of 100 mM and higher.1 Publication
pH dependencei
Optimum pH is 9.0.1 Publication
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Active sitei | 404 | PROSITE-ProRule annotation | 1 | |
Active sitei | 412 | PROSITE-ProRule annotation | 1 | |
Active sitei | 460 | PROSITE-ProRule annotation | 1 | |
Metal bindingi | 597 | Divalent metal cation 1By similarity | 1 | |
Metal bindingi | 599 | Divalent metal cation 1By similarity | 1 | |
Metal bindingi | 647 | Divalent metal cation 1By similarity | 1 | |
Metal bindingi | 647 | Divalent metal cation 2By similarity | 1 | |
Metal bindingi | 680 | Divalent metal cation 2By similarity | 1 | |
Sitei | 681 | Transition state stabilizerBy similarity | 1 | |
Sitei | 684 | Transition state stabilizerBy similarity | 1 | |
Metal bindingi | 792 | Divalent metal cation 2By similarity | 1 | |
Metal bindingi | 824 | Divalent metal cation 2By similarity | 1 | |
Binding sitei | 965 | SubstrateBy similarity | 1 |
GO - Molecular functioni
- 5'-nucleotidase activity Source: GO_Central
- endonuclease activity Source: UniProtKB-KW
- metal ion binding Source: UniProtKB-KW
- nucleotide binding Source: UniProtKB-KW
- UDP-sugar diphosphatase activity Source: GO_Central
GO - Biological processi
- nucleotide catabolic process Source: GO_Central
Keywordsi
Molecular function | Endonuclease, Hydrolase, Nuclease |
Ligand | Calcium, Manganese, Metal-binding, Nucleotide-binding |
Enzyme and pathway databases
BioCyci | BSUB:BSU09190-MONOMER |
Names & Taxonomyi
Protein namesi | |
Gene namesi | Name:yhcR Ordered Locus Names:BSU09190 |
Organismi | Bacillus subtilis (strain 168) |
Taxonomic identifieri | 224308 [NCBI] |
Taxonomic lineagei | Bacteria › Firmicutes › Bacilli › Bacillales › Bacillaceae › Bacillus › |
Proteomesi |
|
Subcellular locationi
Cell wall
- cell wall 3 Publications; Peptidoglycan-anchor PROSITE-ProRule annotation
Note: Anchored to the cell wall by sortase SrtD.2 Publications
Extracellular region or secreted
- extracellular region Source: UniProtKB-KW
Other locations
- outer membrane-bounded periplasmic space Source: GO_Central
Keywords - Cellular componenti
Cell wall, SecretedPTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Signal peptidei | 1 – 46 | Sequence analysisAdd BLAST | 46 | |
ChainiPRO_0000000040 | 47 – 1185 | Endonuclease YhcRAdd BLAST | 1139 | |
PropeptideiPRO_0000445194 | 1186 – 1217 | Removed by sortasePROSITE-ProRule annotationAdd BLAST | 32 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Modified residuei | 1185 | Pentaglycyl murein peptidoglycan amidated threoninePROSITE-ProRule annotation | 1 |
Keywords - PTMi
Peptidoglycan-anchorProteomic databases
PaxDbi | P54602 |
Interactioni
Protein-protein interaction databases
IntActi | P54602, 3 interactors |
STRINGi | 224308.BSU09190 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 376 – 517 | TNase-likePROSITE-ProRule annotationAdd BLAST | 142 |
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 590 – 828 | PhosphoesteraseAdd BLAST | 239 | |
Regioni | 829 – 1085 | 5'-nucleotidaseAdd BLAST | 257 | |
Regioni | 1035 – 1042 | Substrate bindingBy similarity | 8 | |
Regioni | 1087 – 1142 | DisorderedSequence analysisAdd BLAST | 56 |
Motif
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Motifi | 1182 – 1186 | LPXTG sorting signalPROSITE-ProRule annotation | 5 |
Compositional bias
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Compositional biasi | 1092 – 1110 | Acidic residuesSequence analysisAdd BLAST | 19 | |
Compositional biasi | 1111 – 1126 | Basic and acidic residuesSequence analysisAdd BLAST | 16 |
Sequence similaritiesi
In the C-terminal section; belongs to the 5'-nucleotidase family.Curated
Keywords - Domaini
SignalPhylogenomic databases
eggNOGi | COG0737, Bacteria COG1525, Bacteria COG4085, Bacteria |
OMAi | FEFRARE |
Family and domain databases
CDDi | cd07412, MPP_YhcR_N, 1 hit |
Gene3Di | 2.40.50.90, 1 hit 3.60.21.10, 1 hit 3.90.780.10, 1 hit |
InterProi | View protein in InterPro IPR008334, 5'-Nucleotdase_C IPR036907, 5'-Nucleotdase_C_sf IPR006146, 5'-Nucleotdase_CS IPR006179, 5_nucleotidase/apyrase IPR004843, Calcineurin-like_PHP_ApaH IPR019931, LPXTG_anchor IPR029052, Metallo-depent_PP-like IPR012340, NA-bd_OB-fold IPR035437, SNase_OB-fold_sf IPR016071, Staphylococal_nuclease_OB-fold IPR041831, YhcR_N |
PANTHERi | PTHR11575, PTHR11575, 1 hit |
Pfami | View protein in Pfam PF02872, 5_nucleotid_C, 1 hit PF00746, Gram_pos_anchor, 1 hit PF00149, Metallophos, 1 hit PF00565, SNase, 1 hit |
PRINTSi | PR01607, APYRASEFAMLY |
SMARTi | View protein in SMART SM00318, SNc, 1 hit |
SUPFAMi | SSF50199, SSF50199, 1 hit SSF50249, SSF50249, 1 hit SSF55816, SSF55816, 1 hit SSF56300, SSF56300, 1 hit |
PROSITEi | View protein in PROSITE PS00786, 5_NUCLEOTIDASE_2, 1 hit PS50847, GRAM_POS_ANCHORING, 1 hit PS50830, TNASE_3, 1 hit |
i Sequence
Sequence statusi: Complete.
: The displayed sequence is further processed into a mature form. Sequence processingi
P54602-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MLSVEMISRQ NRCHYVYKGG NMMRRILHIV LITALMFLNV MYTFEAVKAA
60 70 80 90 100
EPQQPISIEK AIQQKEGQAL VEGYAVGQAV SPQHYKLTSP FSNDYNVALA
110 120 130 140 150
DRKNKTSPEH ILPVQIPSAF RSQFGLQTNP LLLGKKITVQ GKLENYFNTT
160 170 180 190 200
GLKNVQSMNV TDDTKTPPAE QQVTINEARG RLNEEVTIKG IITADQNAIG
210 220 230 240 250
GGKLSTFLQD ETGGINIYSP SPEQFPELKE GMDVTVTGKI TSYQGLKEIV
260 270 280 290 300
PNSSGIKINQ SNQSLPAPKH LTINELINGS LGDQYEGRLV KLTAFVSSIP
310 320 330 340 350
SSPAGGGYNV TMIDDDHHAM TLRVMNETGV INELDEGKWY EFTGVLSRYQ
360 370 380 390 400
TFQLLPRKSA DLKLLEEQPA PPSAEGEYEG IVDRVVDGDT IHLKSPVLGT
410 420 430 440 450
TKIRFVNVDA PETYHTPKND ADENQLRFGK KASDYLKTVL SPGDKITVKV
460 470 480 490 500
GSEAKDSYGR LLGQVITESG SNVNLELVKN GYAPTYFIWP VDNEEDYQQF
510 520 530 540 550
QAAVAAAKKD QKGIWNENDP LMEMPFEFRA REQGKGLTRY VGDSSNKTYV
560 570 580 590 600
QPADWKKIAV ENRIFFASAS EAESAGYKKR QTAPQEHVPL RILSMNDLHG
610 620 630 640 650
KIDQQYELDL DGNGTVDGTF GRMDYAAAYL KEKKAEKKNS LIVHAGDMIG
660 670 680 690 700
GSSPVSSLLQ DEPTVELMED IGFDVGTVGN HEFDEGTDEL LRILNGGDHP
710 720 730 740 750
KGTSGYDGQN FPLVCANCKM KSTGEPFLPA YDIINVEGVP VAFIGVVTQS
760 770 780 790 800
AAGMVMPEGI KNIEFTDEAT AVNKAAEELK KKGVKAIAVL AHMSAEQNGN
810 820 830 840 850
AITGESADLA NKTDSEIDVI FAAHNHQVVN GEVNGKLIVQ AFEYGKAIGV
860 870 880 890 900
VDVEIDKTTK DIVKKSAEIV YVDQSKIEPD VSASAILKKY ETIAEPIISE
910 920 930 940 950
VVGEAAVDME GGYSNDGDTP LGNLIADGMR AAMKTDFALM NGGGIREALK
960 970 980 990 1000
KGPITWGDLY NIQPFGNVLT KLEIKGKDLR EIINAQISPV FGPDYSISGF
1010 1020 1030 1040 1050
TYTWDKETGK AVDMKMADGT EIQPDATYTL TVNNFMATAT GAKYQPIGLL
1060 1070 1080 1090 1100
GKNPVTGPED LEATVEYVKS FDEPIAYTKE GRIKLAEASD IEDPVTEDPI
1110 1120 1130 1140 1150
TEEPGDDPGT EDPIKEDPRP GEDLPDIKET PGTAPVHQLP PSAISRFNEI
1160 1170 1180 1190 1200
PINNTKTADT ANSISTLPLQ TETAESGSDH QLPDTSAGYY NFMVIGAAVT
1210
LSGTYLYVRR KRSASRT
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | X96983 Genomic DNA Translation: CAA65702.1 AL009126 Genomic DNA Translation: CAB12747.1 |
PIRi | F69823 |
RefSeqi | NP_388800.1, NC_000964.3 WP_010886455.1, NZ_JNCM01000035.1 |
Genome annotation databases
EnsemblBacteriai | CAB12747; CAB12747; BSU_09190 |
GeneIDi | 936241 |
KEGGi | bsu:BSU09190 |
PATRICi | fig|224308.43.peg.960 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | X96983 Genomic DNA Translation: CAA65702.1 AL009126 Genomic DNA Translation: CAB12747.1 |
PIRi | F69823 |
RefSeqi | NP_388800.1, NC_000964.3 WP_010886455.1, NZ_JNCM01000035.1 |
3D structure databases
SMRi | P54602 |
ModBasei | Search... |
Protein-protein interaction databases
IntActi | P54602, 3 interactors |
STRINGi | 224308.BSU09190 |
Proteomic databases
PaxDbi | P54602 |
Genome annotation databases
EnsemblBacteriai | CAB12747; CAB12747; BSU_09190 |
GeneIDi | 936241 |
KEGGi | bsu:BSU09190 |
PATRICi | fig|224308.43.peg.960 |
Phylogenomic databases
eggNOGi | COG0737, Bacteria COG1525, Bacteria COG4085, Bacteria |
OMAi | FEFRARE |
Enzyme and pathway databases
BioCyci | BSUB:BSU09190-MONOMER |
Family and domain databases
CDDi | cd07412, MPP_YhcR_N, 1 hit |
Gene3Di | 2.40.50.90, 1 hit 3.60.21.10, 1 hit 3.90.780.10, 1 hit |
InterProi | View protein in InterPro IPR008334, 5'-Nucleotdase_C IPR036907, 5'-Nucleotdase_C_sf IPR006146, 5'-Nucleotdase_CS IPR006179, 5_nucleotidase/apyrase IPR004843, Calcineurin-like_PHP_ApaH IPR019931, LPXTG_anchor IPR029052, Metallo-depent_PP-like IPR012340, NA-bd_OB-fold IPR035437, SNase_OB-fold_sf IPR016071, Staphylococal_nuclease_OB-fold IPR041831, YhcR_N |
PANTHERi | PTHR11575, PTHR11575, 1 hit |
Pfami | View protein in Pfam PF02872, 5_nucleotid_C, 1 hit PF00746, Gram_pos_anchor, 1 hit PF00149, Metallophos, 1 hit PF00565, SNase, 1 hit |
PRINTSi | PR01607, APYRASEFAMLY |
SMARTi | View protein in SMART SM00318, SNc, 1 hit |
SUPFAMi | SSF50199, SSF50199, 1 hit SSF50249, SSF50249, 1 hit SSF55816, SSF55816, 1 hit SSF56300, SSF56300, 1 hit |
PROSITEi | View protein in PROSITE PS00786, 5_NUCLEOTIDASE_2, 1 hit PS50847, GRAM_POS_ANCHORING, 1 hit PS50830, TNASE_3, 1 hit |
MobiDBi | Search... |
Entry informationi
Entry namei | YHCR_BACSU | |
Accessioni | P54602Primary (citable) accession number: P54602 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | October 1, 1996 |
Last sequence update: | October 1, 1996 | |
Last modified: | February 23, 2022 | |
This is version 149 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
Reference proteomeDocuments
- SIMILARITY comments
Index of protein domains and families