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(-) Description

Title :  MTRUVA FORM III
 
Authors :  J. R. Prabu, S. Thamotharan, J. S. Khanduja, N. R. Chandra, K. Muniyappa M. Vijayan
Date :  01 Oct 08  (Deposition) - 05 May 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Keywords :  Recombination, Branch Migration, Holliday Junction, Dna Binding, Oligomerization, Acidic Pin, Dna Binding Protein, Atp-Binding, Dna Damage, Dna Recombination, Dna Repair, Dna-Binding, Helicase, Hydrolase, Nucleotide-Binding, Sos Response (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. R. Prabu, S. Thamotharan, J. S. Khanduja, N. R. Chandra, K. Muniyappa, M. Vijayan
Crystallographic And Modelling Studies On Mycobacterium Tuberculosis Ruva Additional Role Of Ruvb-Binding Domain An Inter Species Variability
Biochim. Biophys. Acta V. 1794 1001 2009
PubMed-ID: 19374958  |  Reference-DOI: 10.1016/J.BBAPAP.2009.04.003

(-) Compounds

Molecule 1 - HOLLIDAY JUNCTION ATP-DEPENDENT DNA HELICASE RUVA
    ChainsA, B
    EC Number3.6.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMTRA
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneRUVA
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid1773

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (4x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
Biological Unit 1 (1, 16)
No.NameCountTypeFull Name
1GOL16Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:81 , PRO A:82 , ARG A:83 , LEU A:84BINDING SITE FOR RESIDUE GOL A 502
2AC2SOFTWAREARG A:53 , HOH A:565BINDING SITE FOR RESIDUE GOL A 504
3AC3SOFTWAREGLY B:81 , PRO B:82 , ARG B:83 , LEU B:84BINDING SITE FOR RESIDUE GOL B 501
4AC4SOFTWAREALA B:161 , ALA B:162 , LYS B:163BINDING SITE FOR RESIDUE GOL B 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZTD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZTD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZTD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZTD)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZTD)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:189
 aligned with RUVA_MYCTO | P9WGW2 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:202
                                   1                                                                                                                                                                                                  
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193  
           RUVA_MYCTO     - -------MIASVRGEVLEVALDHVVIEAAGVGYRVNATPATLATLRQGTEARLITAMIVREDSMTLYGFPDGETRDLFLTLLSVSGVGPRLAMAALAVHDAPALRQVLADGNVAALTRVPGIGKRGAERMVLELRDKVGVAATGGALSTNGHAVRSPVVEALVGLGFAAKQAEEATDTVLAANHDATTSSALRSALSLLGKA 195
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ztdA01 A:-6-64 Nucleic acid-binding proteins                          2ztdA02 A:65-132 5' to 3' exonuclease, C-terminal subdomain         -------------2ztdA03 A:146-195                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee...eeeeee..eeeeee.hhhhhh......eeeeeeeeeee..eeeeeee.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh....hhhhhhhhhhhhh....-------------.hhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ztd A  -6 MGRGSEFMIASVRGEVLEVALDHVVIEAAGVGYRVNATPATLATLRQGTEARLITAMIVREDSMTLYGFPDGETRDLFLTLLSVSGVGPRLAMAALAVHDAPALRQVLADGNVAALTRVPGIGKRGAERMVLELRDKVG-------------AVRSPVVEALVGLGFAAKQAEEATDTVLAANHDATTSSALRSALSLLGKA 195
                                     3        13        23        33        43        53        63        73        83        93       103       113       123        |-         -  |    153       163       173       183       193  
                                                                                                                                                                    132           146                                                 

Chain A from PDB  Type:PROTEIN  Length:189
 aligned with RUVA_MYCTU | P9WGW3 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:202
                                   1                                                                                                                                                                                                  
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193  
           RUVA_MYCTU     - -------MIASVRGEVLEVALDHVVIEAAGVGYRVNATPATLATLRQGTEARLITAMIVREDSMTLYGFPDGETRDLFLTLLSVSGVGPRLAMAALAVHDAPALRQVLADGNVAALTRVPGIGKRGAERMVLELRDKVGVAATGGALSTNGHAVRSPVVEALVGLGFAAKQAEEATDTVLAANHDATTSSALRSALSLLGKA 195
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ztdA01 A:-6-64 Nucleic acid-binding proteins                          2ztdA02 A:65-132 5' to 3' exonuclease, C-terminal subdomain         -------------2ztdA03 A:146-195                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee...eeeeee..eeeeee.hhhhhh......eeeeeeeeeee..eeeeeee.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh....hhhhhhhhhhhhh....-------------.hhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ztd A  -6 MGRGSEFMIASVRGEVLEVALDHVVIEAAGVGYRVNATPATLATLRQGTEARLITAMIVREDSMTLYGFPDGETRDLFLTLLSVSGVGPRLAMAALAVHDAPALRQVLADGNVAALTRVPGIGKRGAERMVLELRDKVG-------------AVRSPVVEALVGLGFAAKQAEEATDTVLAANHDATTSSALRSALSLLGKA 195
                                     3        13        23        33        43        53        63        73        83        93       103       113       123        |-         -  |    153       163       173       183       193  
                                                                                                                                                                    132           146                                                 

Chain B from PDB  Type:PROTEIN  Length:182
 aligned with RUVA_MYCTO | P9WGW2 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:197
                               1                                                                                                                                                                                                 
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       
           RUVA_MYCTO     - ---MIASVRGEVLEVALDHVVIEAAGVGYRVNATPATLATLRQGTEARLITAMIVREDSMTLYGFPDGETRDLFLTLLSVSGVGPRLAMAALAVHDAPALRQVLADGNVAALTRVPGIGKRGAERMVLELRDKVGVAATGGALSTNGHAVRSPVVEALVGLGFAAKQAEEATDTVLAANHDATTSSALRSALSLLGK 194
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ztdB01 B:-2-64 Nucleic acid-binding proteins                      2ztdB02 B:65-131 5' to 3' exonuclease, C-terminal subdomain        ---------------2ztdB03 B:147-194                                CATH domains
           Pfam domains (1) ---RuvA_N-2ztdB01 B:1-61                                        -------------------------------------------------------------------------------------RuvA_C-2ztdB03 B:147-193                       - Pfam domains (1)
           Pfam domains (2) ---RuvA_N-2ztdB02 B:1-61                                        -------------------------------------------------------------------------------------RuvA_C-2ztdB04 B:147-193                       - Pfam domains (2)
         Sec.struct. author ....eeeeeeeeeee...eeeeee..eeeeee.hhhhhh......eeeeeeeeeee..eeeeeee.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh....hhhhhhhhhhhhh...---------------hhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ztd B  -2 SEFMIASVRGEVLEVALDHVVIEAAGVGYRVNATPATLATLRQGTEARLITAMIVREDSMTLYGFPDGETRDLFLTLLSVSGVGPRLAMAALAVHDAPALRQVLADGNVAALTRVPGIGKRGAERMVLELRDKV---------------VRSPVVEALVGLGFAAKQAEEATDTVLAANHDATTSSALRSALSLLGK 194
                                     7        17        27        37        47        57        67        77        87        97       107       117       127   |     -       147       157       167       177       187       
                                                                                                                                                               131             147                                               

Chain B from PDB  Type:PROTEIN  Length:182
 aligned with RUVA_MYCTU | P9WGW3 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:197
                               1                                                                                                                                                                                                 
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       
           RUVA_MYCTU     - ---MIASVRGEVLEVALDHVVIEAAGVGYRVNATPATLATLRQGTEARLITAMIVREDSMTLYGFPDGETRDLFLTLLSVSGVGPRLAMAALAVHDAPALRQVLADGNVAALTRVPGIGKRGAERMVLELRDKVGVAATGGALSTNGHAVRSPVVEALVGLGFAAKQAEEATDTVLAANHDATTSSALRSALSLLGK 194
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ztdB01 B:-2-64 Nucleic acid-binding proteins                      2ztdB02 B:65-131 5' to 3' exonuclease, C-terminal subdomain        ---------------2ztdB03 B:147-194                                CATH domains
           Pfam domains (1) ---RuvA_N-2ztdB01 B:1-61                                        -------------------------------------------------------------------------------------RuvA_C-2ztdB03 B:147-193                       - Pfam domains (1)
           Pfam domains (2) ---RuvA_N-2ztdB02 B:1-61                                        -------------------------------------------------------------------------------------RuvA_C-2ztdB04 B:147-193                       - Pfam domains (2)
         Sec.struct. author ....eeeeeeeeeee...eeeeee..eeeeee.hhhhhh......eeeeeeeeeee..eeeeeee.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh....hhhhhhhhhhhhh...---------------hhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ztd B  -2 SEFMIASVRGEVLEVALDHVVIEAAGVGYRVNATPATLATLRQGTEARLITAMIVREDSMTLYGFPDGETRDLFLTLLSVSGVGPRLAMAALAVHDAPALRQVLADGNVAALTRVPGIGKRGAERMVLELRDKV---------------VRSPVVEALVGLGFAAKQAEEATDTVLAANHDATTSSALRSALSLLGK 194
                                     7        17        27        37        47        57        67        77        87        97       107       117       127   |     -       147       157       167       177       187       
                                                                                                                                                               131             147                                               

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2ZTD)

(-) CATH Domains  (3, 6)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: OB (224)
(-)
Clan: UBA (32)

(-) Gene Ontology  (15, 28)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RUVA_MYCTU | P9WGW3)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003678    DNA helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA helix.
    GO:0009378    four-way junction helicase activity    Catalysis of the unwinding of the DNA helix of DNA containing four-way junctions, including Holliday junctions.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0032508    DNA duplex unwinding    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0009432    SOS response    An error-prone process for repairing damaged microbial DNA.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0000724    double-strand break repair via homologous recombination    The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule.
cellular component
    GO:0009379    Holliday junction helicase complex    A DNA helicase complex that forms part of a Holliday junction resolvase complex, where the helicase activity is involved in the migration of the junction branch point. The best-characterized example is the E. coli RuvAB complex, in which a hexamer of RuvB subunits possesses helicase activity that is modulated by association with RuvA.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A,B   (RUVA_MYCTO | P9WGW2)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003678    DNA helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA helix.
    GO:0009378    four-way junction helicase activity    Catalysis of the unwinding of the DNA helix of DNA containing four-way junctions, including Holliday junctions.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0032508    DNA duplex unwinding    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0009432    SOS response    An error-prone process for repairing damaged microbial DNA.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
cellular component
    GO:0009379    Holliday junction helicase complex    A DNA helicase complex that forms part of a Holliday junction resolvase complex, where the helicase activity is involved in the migration of the junction branch point. The best-characterized example is the E. coli RuvAB complex, in which a hexamer of RuvB subunits possesses helicase activity that is modulated by association with RuvA.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RUVA_MYCTO | P9WGW22h5x 2ztc 2zte
        RUVA_MYCTU | P9WGW32h5x 2ztc 2zte

(-) Related Entries Specified in the PDB File

2h5x MTRUVA FORM I
2ztc MTRUVA FORM II
2zte MTRUVA FORM IV