Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.cmm.msu.ru/~anuta_al/projects/Zachetnoe.doc Дата изменения: Sun Mar 15 19:49:29 2009 Дата индексирования: Tue Oct 2 13:25:02 2012 Кодировка: koi8-r Поисковые слова: цинк

Зачетное задание.

Информация о белке АТФ зависимая ДНК геликаза-recQ.



Итак, данный белок относится к классу ферментов Гидролазы семейству
ДНК-геликазы, подсемейству RECQ.

Белок участвует в одном из факторов рекомбинации - recF, причём ген
экспрессии находится под регуляцией системы СОС-репарации. Если говорить о
взаимодействии с другими субъединицами, то можно отметить взаимодействие
белка с селенометионином, катионом цинка, ионом марганца II, водой.
Формулы данных лигандов и количество молекул, взаимодействующих с белком
указаны в след таблице:



|ID | Название |Формула |Число копий|Комментарии |
|MSE |SELENOMETHIONINE |C5 H11 N O2|15 |Cеленометионин |
| | |SE | | |
|ZN |ZINC ION |ZN 2+ |1 |Катион цинка |
|MN |MANGANESE (II) ION |MN 2+ |1 |Катион марганца|
|HOH |AQVA |H2 O |708 |Вода |


Взаимодействие лиганда цинка с белком RECQ_Ecoli наглядно показано на
изображении:

[pic]

Что касается особенностей последовательности: молекула белка (ATФ-
зависимая ДНК - хеликаза) содержит одну цепь (цепь А), состоящую из 609
аминокислотных остатков. Мутация участка от 47 до 54 нуклеотидов не
позволит связаться кофактору ATP (Potential). Последовательность в фаста-
формате представлена в следующей таблице:

| |
|>RECQ_ECOLI ATP-dependent DNA helicase |
| |
|MAQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLV |
| |
|VMPTGGGKSLCYQIPALLLNGLTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQ |
| |
|LEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYA |
| |
|ALGQLRQRFPTLPFMALTATADDTTRQDIVRLLGLNDPLIQISSFDRPNIRYMLMEKFK |
| |
|PLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEK |
| |
|FQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFY |
| |
|DPADMAWLRRCLEEKPQGQLQDIERHKLNAMGAFAEAQTCRRLVLLNYFGEGRQEPCGN |
| |
|CDICLDPPKQYDGSTDAQIALSTIGRVNQRFGMGYVVEVIRGANNQRIRDYGHDKLKVY |
| |
|GMGRDKSHEHWVSVIRQLIHLGLVTQNIAQHSALQLTEAARPVLRGESSLQLAVPRIVA |
| |
|LKPKAMQKSFGGNYDRKLFAKLRKLRKSIADESNVPPYVVFNDATLIEMAEQMPITASE |
| |
|MLSVNGVGMRKLERFGKPFMALIRAHVDGDDEE |


Остовная модель цепи:

[pic]

Белок относится к типу «альфа-бета», включает 27 альфа-спиралей, 19
бета-складок и 52 бета-поворота. Окраска белка по структуре:

[pic]

(Альфа-спираль окрашена в малиновый цвет, бета-спираль - в желтый)

RECQ_Ecoli был обнаружен у бактерии Escherichia coli, относящейся к
семейству Интеробактерии. Представляет собой структуру каталитического
ядра recQ.

Идентификаторы записи в PDB для данного белка следующие: 1OYW, 1OYY, 1WUD;
в UniProt: RECQ_ECOLI. Ссылки на статьи про белок (на основании данных
UniProt):

http://www.uniprot.org/citations/3027506, аннотация:

Irino N., Nakayama K., Nakayama H.



A 2,695 bp chromosomal segment of Escherichia coli K12 containing the recQ
gene was sequenced. Analysis of the sequence revealed an open reading frame
thought to represent recQ, with a clockwise direction of transcription
relative to the standard genetic map of E. coli K12 and having a coding
capacity for a protein of Mr 68,350. The -10 region of the presumptive recQ
promoter overlapped the putative terminator for the upstream gene pldA, and
was immediately followed by a 15 bp stretch of DNA bearing a strong
resemblance to the reported sequences of LexA repressor binding sites. This
latter finding suggested the possibility of SOS regulation of recQ gene
expression, which was substantiated by experiments with recQ-lacZ fusions.

http://www.uniprot.org/citations/1379743, аннотация:

Daniels D.L., Plunkett G. III, Burland V.D., Blattner F.R.



The DNA sequence of 91.4 kilobases of the Escherichia coli K-12 genome,
spanning the region between rrnC at 84.5 minutes and rrnA at 86.5 minutes
on the genetic map (85 to 87 percent on the physical map), is described.
Analysis of this sequence identified 82 potential coding regions (open
reading frames) covering 84 percent of the sequenced interval. The
arrangement of these open reading frames, together with the consensus
promoter sequences and terminator-like sequences found by computer
searches, made it possible to assign them to proposed transcriptional
units. More than half the open reading frames correlated with known genes
or functions suggested by similarity to other sequences. Those remaining
encode still unidentified proteins. The sequenced region also contains
several RNA genes and two types of repeated sequence elements were found.
Intergenic regions include three "gray holes," 0.6 to 0.8 kilobases, with
no recognizable functions.

http://www.uniprot.org/citations/9278503, аннотация:

Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley
M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J.,
Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.



The 4,639,221-base pair sequence of Escherichia coli K-12 is presented. Of
4288 protein-coding genes annotated, 38 percent have no attributed
function. Comparison with five other sequenced microbes reveals ubiquitous
as well as narrowly distributed gene families; many families of similar
genes within E. coli are also evident. The largest family of paralogous
proteins contains 80 ABC transporters. The genome as a whole is strikingly
organized with respect to the local direction of replication; guanines,
oligonucleotides possibly related to replication and recombination, and
most genes are so oriented. The genome also contains insertion sequence
(IS) elements, phage remnants, and many other patches of unusual
composition indicating genome plasticity through horizontal transfer.

http://www.uniprot.org/citations/16397293, аннотация:

Riley M., Abe T., Arnaud M.B., Berlyn M.K.B., Blattner F.R., Chaudhuri
R.R., Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T., Mori H., Perna
N.T., Plunkett G. III, Rudd K.E., Serres M.H., Thomas G.H., Thomson N.R.,
Wishart D., Wanner B.L.



The goal of this group project has been to coordinate and bring up-to-date
information on all genes of Escherichia coli K-12. Annotation of the genome
of an organism entails identification of genes, the boundaries of genes in
terms of precise start and end sites, and description of the gene products.
Known and predicted functions were assigned to each gene product on the
basis of experimental evidence or sequence analysis. Since both kinds of
evidence are constantly expanding, no annotation is complete at any moment
in time. This is a snapshot analysis based on the most recent genome
sequences of two E.coli K-12 bacteria. An accurate and up-to-date
description of E.coli K-12 genes is of particular importance to the
scientific community because experimentally determined properties of its
gene products provide fundamental information for annotation of innumerable
genes of other organisms. Availability of the complete genome sequence of
two K-12 strains allows comparison of their genotypes and mutant status of
alleles.

http://www.uniprot.org/citations/16738553, аннотация:

Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo
E., Baba T., Wanner B.L., Mori H., Horiuchi T.



With the goal of solving the whole-cell problem with Escherichia coli K-12
as a model cell, highly accurate genomes were determined for two closely
related K-12 strains, MG1655 and W3110. Completion of the W3110 genome and
comparison with the MG1655 genome revealed differences at 267 sites,
including 251 sites with short, mostly single-nucleotide, insertions or
deletions (indels) or base substitutions (totaling 358 nucleotides), in
addition to 13 sites with an insertion sequence element or defective
prophage in only one strain and two sites for the W3110 inversion. Direct
DNA sequencing of PCR products for the 251 regions with short indel and
base disparities revealed that only eight sites are true differences. The
other 243 discrepancies were due to errors in the original MG1655 sequence,
including 79 frameshifts, one amino-acid residue deletion, five amino-acid
residue insertions, 73 missense, and 17 silent changes within coding
regions. Errors in the original MG1655 sequence (<1 per 13,000 bases) were
mostly within portions sequenced with out-dated technology based on
radioactive chemistry.

http://www.uniprot.org/citations/2164680, аннотация:

Escherichia coli RecQ protein is a DNA helicase. UniProtKB (1) rdf/xml

Umezu K., Nakayama K., Nakayama H.



The Escherichia coli recQ gene, a member of the RecF recombination gene
family, was set in an overexpression plasmid, and its product was purified
to near-homogeneity. The purified RecQ protein exhibited a DNA-dependent
ATPase and a helicase activity. Without DNA, no ATPase activity was
detected. The capacity as ATPase cofactor varied with the type of DNA in
the following order: circular single strand greater than linear single
strand much greater than circular or linear duplex. As a helicase, RecQ
protein displaced an annealed 71-base or 143-base single-stranded fragment
from circular or linear phage M13 DNA, and the direction of unwinding
seemed to be 3'----5' with respect to the DNA single strand to which the
enzyme supposedly bound. Furthermore, the protein could unwind 143-base-
pair blunt-ended duplex DNA at a higher enzyme concentration. It is
concluded that RecQ protein is a previously unreported helicase, which
might possibly serve to generate single-stranded tails for a strand
transfer reaction in the process of recombination.