Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.cmm.msu.ru/~martiran/projects/MurD2/MurD.doc Дата изменения: Mon Mar 16 03:04:04 2009 Дата индексирования: Tue Oct 2 18:13:56 2012 Кодировка: koi8-r

Отчет о белке Murd_ecoli.

Полное название белка: Уридиндифосфат-N-ацетилмурамоил-L-аланин: D-
глутамат лигаза. Белок относится к классу лигаз и группе белков murCDEF.
Локализируется в цитоплазме бактерий Escherichia coli (Таксономия: Bacteria
- Proteobacteria - Gammaproteobacteria - Enterobacteriales -
Enterobacteriaceae - Escherichia).
В клетке белок осуществляет один из этапов синтеза клеточной стенки, а
именно катализ присоединения глутамата предшественнику нуклеотда УДФ-N-
ацетилмурамоил-L-аланину по формуле:
ATP + UDP-N-acetylmuramoyl-L-alanine + glutamate = ADP + phosphate + UDP-N-
acetylmuramoyl-L-alanyl-D- glutamate.

[pic]
[pic]


Структура белка представляет собой одну цепь, уложенную в структуру,
показанную не рисунке (красным на рисунке отмечены альфа-спирали, а желтым
бета-тяжи). Длинна этой цепи составляет 438 аминокислотных остатка, а
молекулярная масса 46,974 дальтона. С 112 по 118 аминокислотный остаток
последовательности лежит центр связывания молекулы АТФ.
Данные по количеству альфа-спиралей, бета-тяжей и остальных элементов
вторичной структуры в различных базах данных несколько расходятся. В общем
случае различают 20 бета-тяжей и 23 альфа-спирали, а также множество
различных более коротких элементов вторчной структуры.


Полная последовательность белка в формате fasta:
>sp|P14900|MURD_ECOLI UDP-N-acetylmuramoylalanine--D-glutamate ligase;
MADYQGKNVVIIGLGLTGLSCVDFFLARGVTPRVMDTRMTPPGLDKLPEAVERHTGSLNDEWLMAADLIVASPGIA
LAHPSLSAAADAGIEIVGDIELFCREAQAPIVAITGSNGKSTVTTLVGEMAKAAGVNVGVGGNIGLPALMLLDDEC
ELYVLELSSFQLETTSSLQAVAATILNVTEDHMDRYPFGLQQYRAAKLRIYENAKVCVVNADDALTMPIRGADERC
VSFGVNMGDYHLNHQQGETWLRVKGEKVLNVKEMKLSGQHNYTNALAALALADAAGLPRASSLKALTTFTGLPHRF
EVVLEHNGVRWINDSKATNVGSTEAALNGLHVDGTLHLLLGGDGKSADFSPLARYLNGDNVRLYCFGRDGAQLAAL
RPEVAEQTETMEQAMRLLAPRVQPGDMVLLSPACASLDQFKNFEQRGNEFARLAKELG


*Большинство данных о белке и некоторые рисунки взяты с сайта UniProt
(http://www.uniprot.org), PubSUM EMBL (http://www.ebi.ac.uk/pdbsum) и RSCB
PDB (http://www.rcsb.org)


Подробнее о белке можно узнать из записей с сайтов UniProt:
http://www.uniprot.org/uniprot/P14900
А также RSCB PDB
http://www.rcsb.org/pdb/explore.do?structureId=1EEH

Статьи о белке (англ).
Статьи представлены в виде названий, или аннотаций.

1. Nucleotide sequence involving murD and an open reading frame ORF-Y
spacing murF and ftsW in Escherichia coli.

Ikeda M., Wachi M., Ishino F., Matsuhashi M.

Nucleic Acids Res. 18:1058-1058(1990)
2. Nucleotide sequence of the murD gene encoding the UDP-MurNAc-L-Ala-D-Glu
synthetase of Escherichia coli.

Mengin-Lecreulx D., van Heijenoort J.

Nucleic Acids Res. 18:183-183(1990)
3. Systematic sequencing of the Escherichia coli genome: analysis of the 0-
2.4 min region.
Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K.,
Mizobuchi K., Nakata A.
A contiguous 111,402-nucleotide sequence corresponding to the 0 to 2.4 min
region of the E. coli chromosome was determined as a first step to complete
structural analysis of the genome. The resulting sequence was used to
predict open reading frames and to search for sequence similarity against
the PIR protein database. A number of novel genes were found whose
predicted protein sequences showed significant homology with known proteins
from various organisms, including several clusters of genes similar to
those involved in fatty acid metabolism in bacteria (e.g., betT, baiF) and
higher organisms, iron transport (sfuA, B, C) in Serratia marcescens, and
symbiotic nitrogen fixation or electron transport (fixA, B, C, X) in
Azorhizobium caulinodans. In addition, several genes and IS elements that
had been mapped but not sequenced (e.g., leuA, B, C, D) were identified. We
estimate that about 90 genes are represented in this region of the
chromosome with little spacer.
Nucleic Acids Res. 20:3305-3308(1992)
4. The complete genome sequence of Escherichia coli K-12.
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.
Science 277:1453-1474(1997)
5. Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
and W3110.
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.
Mol. Syst. Biol. 2:E1-E5(2006)
6. Structural similarity among Escherichia coli FtsW and RodA proteins and
Bacillus subtilis SpoVE protein, which function in cell division, cell
elongation, and spore formation, respectively.
Ikeda M., Sato T., Wachi M., Jung H.K., Ishino F., Kobayashi Y., Matsuhashi
M.
The Escherichia coli cell division gene ftsW (2 min) was cloned and
sequenced. It encodes a hydrophobic protein(s) with 414 and/or 384 amino
acid residues. The deduced amino acid sequence and the hydropathy profile
of the protein showed high homology with those of the E. coli RodA protein
functioning in determination of the cell shape and the Bacillus subtilis
SpoVE protein functioning in spore formation. Probably similar functional
membrane proteins are involved in these three cell cycle process.
J. Bacteriol. 171:6375-6378(1989)
7. Over-production, purification and properties of the uridine diphosphate
N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli.
Pratviel-Sosa F., Mengin-Lecreulx D., van Heijenoort J.
The UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase of Escherichia coli
was over-produced in strains that harbour recombinant plasmids bearing the
murD gene under the control of the lac or PR promoter. Purification to
homogeneity was achieved by a two-step procedure from a 181-fold over-
producing strain. The N-terminal sequence of the purified protein was
determined and correlated with the nucleotide sequence of the murD gene.
The purified activity was highly dependent on the concentration of
potassium phosphate and Mg2+. The enzyme also catalysed the reverse
reaction. The Km values for UDP-N-acetylmuramoyl-L-alanine; D-glutamate and
ATP/Mg2+ were estimated at 7.5, 55 and 138 microM, respectively. Under the
most optimal in vitro conditions determined, a turnover number of 931 min-1
was estimated. When considering the plasmid-free parental strain, the copy
number of the murD gene product was not more than 1000.cell-1.
8. Crystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
from Escherichia coli.
Bertrand J.A., Auger G., Fanchon E., Martin L., Blanot D., van Heijenoort
J., Dideberg O.
UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (MurD) is a cytoplasmic
enzyme involved in the biosynthesis of peptidoglycan which catalyzes the
addition of D-glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-
alanine (UMA). The crystal structure of MurD in the presence of its
substrate UMA has been solved to 1.9 A resolution. Phase information was
obtained from multiple anomalous dispersion using the K-shell edge of
selenium in combination with multiple isomorphous replacement. The
structure comprises three domains of topology each reminiscent of
nucleotide-binding folds: the N- and C-terminal domains are consistent with
the dinucleotide-binding fold called the Rossmann fold, and the central
domain with the mononucleotide-binding fold also observed in the GTPase
family. The structure reveals the binding site of the substrate UMA, and
comparison with known NTP complexes allows the identification of residues
interacting with ATP. The study describes the first structure of the UDP-N-
acetylmuramoyl-peptide ligase family.
EMBO J. 16:3416-3425(1997)
9. 'Open' structures of MurD: domain movements and structural similarities
with folylpolyglutamate synthetase.
Bertrand J.A., Fanchon E., Martin L., Chantalat L., Auger G., Blanot D.,
van Heijenoort J., Dideberg O.
UDP-N-acetylmuramoyl-l-alanine:d-glutamate (MurD) ligase catalyses the
addition of d-glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-l-
alanine (UMA). The crystal structures of Escherichia coli in the substrate-
free form and MurD complexed with UMA have been determined at 2.4 A and
1.88 A resolution, respectively. The MurD structure comprises three domains
each of a topology reminiscent of nucleotide-binding folds. In the two
structures the C-terminal domain undergoes a large rigid-body rotation away
from the N-terminal and central domains. These two "open" structures were
compared with the four published "closed" structures of MurD. In addition
the comparison reveals which regions are affected by the binding of UMA,
ATP and d-Glu. Also we compare and discuss two structurally characterized
enzymes which belong to the same ligase superfamily: MurD and
folylpolyglutamate synthetase (FGS). The analysis allows the identification
of key residues involved in the reaction mechanism of FGS. The
determination of the two "open" conformation structures represents a new
step towards the complete elucidation of the enzymatic mechanism of the
MurD ligase.
J. Mol. Biol. 301:1257-1266(2000)



Мартынов Александр, 2009 г.