PDBsum entry 1g18

Hydrolase

PDB id

1g18

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Contents

			Protein chain

					310 a.a. *

			Ligands

					ALF-ADP

* Residue conservation analysis

PDB id:

1g18

Links

Name:

Hydrolase

Title:

Reca-adp-alf4 complex

Structure:

Reca protein. Chain: a. Synonym: recombination protein reca. Ec: 3.1.-.-

Source:

Mycobacterium tuberculosis. Organism_taxid: 1773

Resolution:

3.80Å

R-factor:

0.215

R-free:

0.277

Authors:

S.Datta,M.M.Prabu,M.B.Vaze,N.Ganesh,N.R.Chandra,K.Muniyappa, M.Vijayan,Tb Structural Genomics Consortium (Tbsgc)

Key ref:

S.Datta et al. (2000). Crystal structures of Mycobacterium tuberculosis RecA and its complex with ADP-AlF(4): implications for decreased ATPase activity and molecular aggregation. Nucleic Acids Res, 28, 4964-4973. PubMed id: 11121488 DOI: 10.1093/nar/28.24.4964

Date:

11-Oct-00

Release date:

11-Dec-00

PROCHECK

	Headers

	References

Protein chain

P9WHJ3 (RECA_MYCTU) - Protein RecA from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: Struc:

Seq: Struc:					790 a.a. 310 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 68 residue positions (black crosses)



		Enzyme reactions

Enzyme class:

E.C.3.1.-.-

[IntEnz] [ExPASy] [KEGG] [BRENDA]

DOI no: 10.1093/nar/28.24.4964	Nucleic Acids Res 28:4964-4973 (2000)
PubMed id: 11121488

Crystal structures of Mycobacterium tuberculosis RecA and its complex with ADP-AlF(4): implications for decreased ATPase activity and molecular aggregation.
S.Datta, M.M.Prabu, M.B.Vaze, N.Ganesh, N.R.Chandra, K.Muniyappa, M.Vijayan.

ABSTRACT

Sequencing of the complete genome of Mycobacterium tuberculosis, combined with the rapidly increasing need to improve tuberculosis management through better drugs and vaccines, has initiated extensive research on several key proteins from the pathogen. RecA, a ubiquitous multifunctional protein, is a key component of the processes of homologous genetic recombination and DNA repair. Structural knowledge of MtRecA is imperative for a full understanding of both these activities and any ensuing application. The crystal structure of MtRecA, presented here, has six molecules in the unit cell forming a 6(1) helical filament with a deep groove capable of binding DNA. The observed weakening in the higher order aggregation of filaments into bundles may have implications for recombination in mycobacteria. The structure of the complex reveals the atomic interactions of ADP-AlF(4), an ATP analogue, with the P-loop-containing binding pocket. The structures explain reduced levels of interactions of MtRecA with ATP, despite sharing the same fold, topology and high sequence similarity with EcRecA. The formation of a helical filament with a deep groove appears to be an inherent property of MtRecA. The histidine in loop L1 appears to be positioned appropriately for DNA interaction.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21458462

V.E.Galkin, R.L.Britt, L.B.Bane, X.Yu, M.M.Cox, and E.H.Egelman (2011).
Two modes of binding of DinI to RecA filament provide a new insight into the regulation of SOS response by DinI protein.

J Mol Biol, 408, 815-824.

19296440

B.Taneja, J.Yadav, T.K.Chakraborty, and S.K.Brahmachari (2009).
An Indian effort towards affordable drugs: "generic to designer drugs".

Biotechnol J, 4, 348-360.

19465774

Y.Li, Y.He, and Y.Luo (2009).
Conservation of a conformational switch in RadA recombinase from Methanococcus maripaludis.

Acta Crystallogr D Biol Crystallogr, 65, 602-610.

PDB codes:

3etl 3ew9 3ewa

19020353

J.R.Prabu, G.P.Manjunath, N.R.Chandra, K.Muniyappa, and M.Vijayan (2008).
Functionally important movements in RecA molecules and filaments: studies involving mutation and environmental changes.

Acta Crystallogr D Biol Crystallogr, 64, 1146-1157.

PDB codes:

2zr0 2zr7 2zr9 2zra 2zrb 2zrc 2zrd 2zre 2zrf 2zrg 2zrh 2zri 2zrj 2zrk 2zrl 2zrm 2zrn 2zro 2zrp

18637199

P.M.Keller, E.C.Böttger, and P.Sander (2008).
Tuberculosis vaccine strain Mycobacterium bovis BCG Russia is a natural recA mutant.

BMC Microbiol, 8, 120.

18453691

P.S.Kaushal, R.K.Talawar, P.D.Krishna, U.Varshney, and M.Vijayan (2008).
Unique features of the structure and interactions of mycobacterial uracil-DNA glycosylase: structure of a complex of the Mycobacterium tuberculosis enzyme in comparison with those from other sources.

Acta Crystallogr D Biol Crystallogr, 64, 551-560.

PDB code:

2zhx

18461484

S.H.Leuba, S.P.Anand, J.M.Harp, and S.A.Khan (2008).
Expedient placement of two fluorescent dyes for investigating dynamic DNA protein interactions in real time.

Chromosome Res, 16, 451-467.

17713065

K.Okoshi, T.Nishinaka, Y.Doi, R.Hara, M.Hashimoto, and E.Yashima (2007).
Liquid crystal formation of RecA-DNA filamentous complexes.

Chem Commun (Camb), (), 2022-2024.

17228330

M.M.Cox (2007).
Motoring along with the bacterial RecA protein.

Nat Rev Mol Cell Biol, 8, 127-138.

16880543

J.R.Prabu, S.Thamotharan, J.S.Khanduja, E.Z.Alipio, C.Y.Kim, G.S.Waldo, T.C.Terwilliger, B.Segelke, T.Lekin, D.Toppani, L.W.Hung, M.Yu, E.Bursey, K.Muniyappa, N.R.Chandra, and M.Vijayan (2006).
Structure of Mycobacterium tuberculosis RuvA, a protein involved in recombination.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 731-734.

PDB code:

2h5x

16909421

M.Petukhov, D.Lebedev, V.Shalguev, A.Islamov, A.Kuklin, V.Lanzov, and V.Isaev-Ivanov (2006).
Conformational flexibility of RecA protein filament: transitions between compressed and stretched states.

Proteins, 65, 296-304.

16946478

M.Selvaraj, N.S.Singh, S.Roy, R.Sangeetha, U.Varshney, and M.Vijayan (2006).
Cloning, expression, purification, crystallization and preliminary X-ray analysis of peptidyl-tRNA hydrolase from Mycobacterium tuberculosis.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 913-915.

16483938

M.Spies, and S.C.Kowalczykowski (2006).
The RecA binding locus of RecBCD is a general domain for recruitment of DNA strand exchange proteins.

Mol Cell, 21, 573-580.

17142904

P.Singh, R.K.Talawar, P.D.Krishna, U.Varshney, and M.Vijayan (2006).
Overexpression, purification, crystallization and preliminary X-ray analysis of uracil N-glycosylase from Mycobacterium tuberculosis in complex with a proteinaceous inhibitor.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1231-1234.

16648362

R.Krishna, G.P.Manjunath, P.Kumar, A.Surolia, N.R.Chandra, K.Muniyappa, and M.Vijayan (2006).
Crystallographic identification of an ordered C-terminal domain and a second nucleotide-binding site in RecA: new insights into allostery.

Nucleic Acids Res, 34, 2186-2195.

PDB code:

2g88

16699190

S.Das, P.Kumar, V.Bhor, A.Surolia, and M.Vijayan (2006).
Invariance and variability in bacterial PanK: a study based on the crystal structure of Mycobacterium tuberculosis PanK.

Acta Crystallogr D Biol Crystallogr, 62, 628-638.

PDB codes:

2ges 2get 2geu 2gev

16765891

V.E.Galkin, Y.Wu, X.P.Zhang, X.Qian, Y.He, X.Yu, W.D.Heyer, Y.Luo, and E.H.Egelman (2006).
The Rad51/RadA N-terminal domain activates nucleoprotein filament ATPase activity.

Structure, 14, 983-992.

PDB code:

2gdj

15755748

A.Ariza, D.J.Richard, M.F.White, and C.S.Bond (2005).
Conformational flexibility revealed by the crystal structure of a crenarchaeal RadA.

Nucleic Acids Res, 33, 1465-1473.

PDB code:

2bke

16194225

C.E.Bell (2005).
Structure and mechanism of Escherichia coli RecA ATPase.

Mol Microbiol, 58, 358-366.

16041080

K.Saikrishnan, G.P.Manjunath, P.Singh, J.Jeyakanthan, Z.Dauter, K.Sekar, K.Muniyappa, and M.Vijayan (2005).
Structure of Mycobacterium smegmatis single-stranded DNA-binding protein and a comparative study involving homologus SSBs: biological implications of structural plasticity and variability in quaternary association.

Acta Crystallogr D Biol Crystallogr, 61, 1140-1148.

PDB codes:

1x3e 1x3f 1x3g

16508093

S.Das, P.Kumar, V.Bhor, A.Surolia, and M.Vijayan (2005).
Expression, purification, crystallization and preliminary X-ray crystallographic analysis of pantothenate kinase from Mycobacterium tuberculosis.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 65-67.

15956102

T.Akiba, N.Ishii, N.Rashid, M.Morikawa, T.Imanaka, and K.Harata (2005).
Structure of RadB recombinase from a hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1: an implication for the formation of a near-7-fold helical assembly.

Nucleic Acids Res, 33, 3412-3423.

PDB codes:

2cvf 2cvh

15235592

A.B.Conway, T.W.Lynch, Y.Zhang, G.S.Fortin, C.W.Fung, L.S.Symington, and P.A.Rice (2004).
Crystal structure of a Rad51 filament.

Nat Struct Mol Biol, 11, 791-796.

PDB code:

1szp

14747728

K.Saikrishnan, S.K.Kalapala, M.Bidya Sagar, A.R.Rao, U.Varshney, and M.Vijayan (2004).
Purification, crystallization and preliminary X-ray studies of Mycobacterium tuberculosis RRF.

Acta Crystallogr D Biol Crystallogr, 60, 368-370.

12941707

D.S.Shin, L.Pellegrini, D.S.Daniels, B.Yelent, L.Craig, D.Bates, D.S.Yu, M.K.Shivji, C.Hitomi, A.S.Arvai, N.Volkmann, H.Tsuruta, T.L.Blundell, A.R.Venkitaraman, and J.A.Tainer (2003).
Full-length archaeal Rad51 structure and mutants: mechanisms for RAD51 assembly and control by BRCA2.

EMBO J, 22, 4566-4576.

PDB code:

1pzn

12915092

M.Bellinzoni, and G.Riccardi (2003).
Techniques and applications: The heterologous expression of Mycobacterium tuberculosis genes is an uphill road.

Trends Microbiol, 11, 351-358.

14527291

M.M.Cox (2003).
The bacterial RecA protein as a motor protein.

Annu Rev Microbiol, 57, 551-577.

14654697

N.Acharya, R.K.Talawar, K.Saikrishnan, M.Vijayan, and U.Varshney (2003).
Substitutions at tyrosine 66 of Escherichia coli uracil DNA glycosylase lead to characterization of an efficient enzyme that is recalcitrant to product inhibition.

Nucleic Acids Res, 31, 7216-7226.

12945045

N.Ganesh, and K.Muniyappa (2003).
Mycobacterium smegmatis RecA protein is structurally similar to but functionally distinct from Mycobacterium tuberculosis RecA.

Proteins, 53, 6.

12586392

R.E.Marquis, S.A.Clock, and M.Mota-Meira (2003).
Fluoride and organic weak acids as modulators of microbial physiology.

FEMS Microbiol Rev, 26, 493-510.

12557189

S.Datta, N.Ganesh, N.R.Chandra, K.Muniyappa, and M.Vijayan (2003).
Structural studies on MtRecA-nucleotide complexes: insights into DNA and nucleotide binding and the structural signature of NTP recognition.

Proteins, 50, 474-485.

PDB codes:

1mo3 1mo4 1mo5 1mo6

12837805

S.Datta, R.Krishna, N.Ganesh, N.R.Chandra, K.Muniyappa, and M.Vijayan (2003).
Crystal structures of Mycobacterium smegmatis RecA and its nucleotide complexes.

J Bacteriol, 185, 4280-4284.

PDB codes:

1ubc 1ube 1ubf 1ubg

11896404

Madhusudan, P.Akamine, N.H.Xuong, and S.S.Taylor (2002).
Crystal structure of a transition state mimic of the catalytic subunit of cAMP-dependent protein kinase.

Nat Struct Biol, 9, 273-277.

PDB code:

1l3r

12218174

R.Venkatesh, N.Ganesh, N.Guhan, M.S.Reddy, T.Chandrasekhar, and K.Muniyappa (2002).
RecX protein abrogates ATP hydrolysis and strand exchange promoted by RecA: insights into negative regulation of homologous recombination.

Proc Natl Acad Sci U S A, 99, 12091-12096.

12045091

S.L.Lusetti, and M.M.Cox (2002).
The bacterial RecA protein and the recombinational DNA repair of stalled replication forks.

Annu Rev Biochem, 71, 71.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.