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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR880 IGR885 IGR884 IGR879 IGR881 IGR882 IGR889 IGR878 IGR886 IGR888 IGR883 IGR887 HD1207 HD1200 smpA, - HD1212 HD1211 HD1214 waaQ, - HD1202 HD1203 HD1215 rnh,rnhA, - HD1206 cvpA,dedE, - HD1208 lapB, - HD1205 lgtF, - HD1201 purF, - HD1209 argG, - HD1204 HD1207 HD1200 smpA, - HD1212 HD1211 HD1214 waaQ, - HD1202 HD1203 HD1215 rnh,rnhA, - HD1206 cvpA,dedE, - HD1208 lapB, - HD1205 lgtF, - HD1201 purF, - HD1209 argG, - HD1204 HD1207 HD1200 smpA, - HD1212 HD1211 HD1214 waaQ, - HD1202 HD1213 HD1213 HD1203 HD1215 rnh,rnhA, - HD1206 cvpA,dedE, - HD1208 lapB, - HD1205 lgtF, - HD1201 purF, - HD1209 argG, - HD1204 purF, - HD1210 purF, - HD1210
* Calculated from Protein Sequence

Gene ID: HD1206

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
rnh  rnhA  

Definition:
ribonuclease H

Gene Start:
981500

Gene Stop:
981961

Gene Length:
462

Molecular Weight*:
17437

pI*:
9.60

Net Charge*:
5.81

EC:
3.1.26.4  

Functional Class:
Transcription; Degradation of RNA  

Pathway: pathway table

Secondary Evidence:
Kanaya,S., Kimura,S., Katsuda,C. and Ikehara,M.
Role of cysteine residues in ribonuclease H from Escherichia coli.
Site-directed mutagenesis and chemical modification
The Biochemical journal. 271 (1), 59-66 (1990)
MEDLINE: 91024947

Katayanagi,K., Miyagawa,M., Matsushima,M., Ishikawa,M., Kanaya,S.,
Ikehara,M., Matsuzaki,T. and Morikawa,K.
Three-dimensional structure of ribonuclease H from E. coli
Nature. 347 (6290), 306-309 (1990)
MEDLINE: 90384573

Katayanagi,K., Miyagawa,M., Matsushima,M., Ishikawa,M., Kanaya,S.,
Nakamura,H., Ikehara,M., Matsuzaki,T. and Morikawa,K.
Structural details of ribonuclease H from Escherichia coli as
refined to an atomic resolution
Journal of molecular biology. 223 (4), 1029-1052 (1992)
MEDLINE: 92167248

Yang,W., Hendrickson,W.A., Crouch,R.J. and Satow,Y.
Structure of ribonuclease H phased at 2 A resolution by MAD
analysis of the selenomethionyl protein
Science. 249 (4975), 1398-1405 (1990)
MEDLINE: 90385276

Ishikawa,K., Kimura,S., Kanaya,S., Morikawa,K. and Nakamura,H.
Structural study of mutants of Escherichia coli ribonuclease HI
with enhanced thermostability
Protein engineering. 6 (1), 85-91 (1993)
MEDLINE: 93165655

Katayanagi,K., Ishikawa,M., Okumura,M., Ariyoshi,M., Kanaya,S.,
Kawano,Y., Suzuki,M., Tanaka,I. and Morikawa,K.
Crystal structures of ribonuclease HI active site mutants from
Escherichia coli
The Journal of biological chemistry. 268 (29), 22092-22099 (1993)
MEDLINE: 94012805

Kashiwagi,T., Jeanteur,D., Haruki,M., Katayanagi,K., Kanaya,S. and
Morikawa,K.
Proposal for new catalytic roles for two invariant residues in
Escherichia coli ribonuclease HI
Protein engineering. 9 (10), 857-867 (1996)
MEDLINE: 97084791

Yamazaki,T., Yoshida,M., Kanaya,S., Nakamura,H. and Nagayama,K.
Assignments of backbone 1H, 13C, and 15N resonances and secondary
structure of ribonuclease H from Escherichia coli by heteronuclear
three-dimensional NMR spectroscopy
Biochemistry. 30 (24), 6036-6047 (1991)
MEDLINE: 91255229

Yamasaki,K., Ogasahara,K., Yutani,K., Oobatake,M. and Kanaya,S.
Folding pathway of Escherichia coli ribonuclease HI: a circular
dichroism, fluorescence, and NMR study
Biochemistry. 34 (51), 16552-16562 (1995)
MEDLINE: 96118372


Comment:
For the rnhB gene (HII) see HD1026.

Blast Summary:  PSI-Blast Search
This sequence corresponds to the previously reported gi 148978 in GenBank.

Numerous significant hits using gapped BLAST to ribomnuclease H from H. influenzae (1173097), Salmonella typhimurium (133164), E. coli (133163), among others.

HD1206 is similar to ribonuclease H from T. pallidum (TP0353). No similarities to C. trachomatis, C. pneumoniae, U. urealyticum, M. genitalium, or M. pneumoniae.


COGS Summary:  COGS Search
BeTs to 8 clades of COG0328
COG name: Ribonuclease HI
Functional Class: L
The phylogenetic pattern of COG0328 is ----y--cebrhuj---l--x
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
***** IPB002156 (RNase H) with a combined E-value of 1.3e-11.
    IPB002156A    6-16
    IPB002156B    63-73
    IPB002156C    128-137


ProDom Summary:  Protein Domain Search
Residues 6-137 are 48% similar to a (POLYPROTEIN PROTEASE HYDROLASE DNA) protein domain (PD000727) which is seen in Q9PM39_CAMJE.

Residues 98-147 are 50% similar to a (RIBONUCLEASE RNASE MAGNESIUM ENDONUCLEASE) protein domain (PD300097) which is seen in RNH_BUCAP.

Residues 2-110 are 75% similar to a (RIBONUCLEASE RNASE HYDROLASE MAGNESIUM) protein domain (PD334831) which is seen in RNH_PASMU.



Paralogs:  Local Blast Search

HD1206 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 1 to 141 (E-value = 2e-58) place HD1206 in the RnaseH family which is described as RNase H (PF00075)

PDB Hit:
pdb|1RBT| Ribonuclease H (E.C.3.1.26.4) Mutant With Lys 95 R... 210 1e-055
pdb|1RBS| Ribonuclease H (E.C.3.1.26.4) Mutant With His 62 R... 209 2e-055
pdb|1RBV| Ribonuclease H (E.C.3.1.26.4) Mutant With Lys 95 R... 207 5e-055

Gene Protein Sequence:
MKSVNIFTDGSCLGNPGPGGIGVVLRYNQHQKKVSQGYFQTTNNRMELRA
VIEGLSMLKEACNVTLYSDSQYMKNGITKWIFKWKKSNWKTANGKAVKNK
DLWLLLDEKIQIHYIEWKWVKGHSGHYENEICDELAKLGANNPTLEDVGY
QPA$

Gene Nucleotide Sequence:  Sequence Viewer
ATGAAATCAGTTAACATTTTTACCGATGGTTCTTGTTTGGGAAATCCTGG
TCCTGGCGGAATTGGTGTAGTATTACGTTATAATCAGCATCAGAAAAAAG
TGAGTCAAGGATATTTTCAAACAACGAATAATCGTATGGAATTACGCGCA
GTAATTGAAGGGCTTTCAATGTTAAAAGAAGCCTGTAATGTAACCCTTTA
TTCAGACAGTCAATATATGAAAAATGGGATTACTAAATGGATCTTTAAGT
GGAAAAAATCGAACTGGAAAACAGCAAATGGTAAAGCGGTCAAGAATAAA
GATCTTTGGTTATTATTGGATGAAAAAATTCAAATACATTATATAGAATG
GAAATGGGTAAAGGGGCACTCAGGCCATTATGAAAATGAAATATGCGATG
AACTGGCTAAACTCGGCGCAAATAACCCAACGTTAGAAGATGTTGGTTAT
CAGCCCGCATAA


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