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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MINIMAL RELAXASE DOMAIN OF MOBA FROM PLASMID R1162
 
Authors :  A. F. Monzingo, A. Ozburn, S. Xia, R. J. Meyer, J. D. Robertus
Date :  03 Nov 06  (Deposition) - 06 Feb 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Nickase, 5-Strand Antiparallel Beta Sheet, Metalloenzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. F. Monzingo, A. Ozburn, S. Xia, R. J. Meyer, J. D. Robertus
The Structure Of The Minimal Relaxase Domain Of Moba At 2. 1 A Resolution.
J. Mol. Biol. V. 366 165 2007
PubMed-ID: 17157875  |  Reference-DOI: 10.1016/J.JMB.2006.11.031
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MOBILIZATION PROTEIN A
    ChainsA
    EC Number3.6.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTYB2
    Expression System StrainK-12 STRAIN ER2566
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentMINIMAL RELAXASE DOMAIN
    GeneMOBA
    Organism ScientificPSEUDOMONAS AERUGINOSA
    Organism Taxid287

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1MN3Ligand/IonMANGANESE (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:112 , HIS A:120 , HIS A:122 , HOH A:1024BINDING SITE FOR RESIDUE MN A 1001
2AC2SOFTWAREHIS A:46 , GLN A:97 , HOH A:1025BINDING SITE FOR RESIDUE MN A 1002
3AC3SOFTWAREGLU A:52 , HIS A:98 , HIS A:176BINDING SITE FOR RESIDUE MN A 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NS6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2NS6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2NS6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2NS6)

(-) Exons   (0, 0)

(no "Exon" information available for 2NS6)

(-) Sequences/Alignments

Asymmetric/Biological 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:183
 aligned with D0VWX2_PSEAI | D0VWX2 from UniProtKB/TrEMBL  Length:185

    Alignment length:185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     
         D0VWX2_PSEAI     1 AIYHLTAKTGSRSGGQSARAKADYIQREGKYARDMDEVLHAESGHMPEFVERPADYWDAADLYERANGRLFKEVEFALPVELTLDQQKALASEFAQHLTGAERLPYTLAIHAGGGENPHCHLMISERINDGIERPAAQWFKRYNGKTPEKGGAQKTEALKPKAWLEQTREAWADHANRALERAGH 185
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------MobA_MobL-2ns6A01 A:17-186                                                                                                                                                 Pfam domains
         Sec.struct. author ....eeeeee.--...hhhhhhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhh......eeeeeee.....hhhhhhhhhhhhhhhhhh.....eeeeeeee...eeeeeeee..........hhhhhh......hhhhh...........hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ns6 A   2 AIYHLTAKTGS--GGQSARAKADYIQREGKYARDMDEVLHAESGHMPEFVERPADYWDAADLYERANGRLFKEVEFALPVELTLDQQKALASEFAQHLTGAERLPYTLAIHAGGGENPHCHLMISERINDGIERPAAQWFKRYNGKTPEKGGAQKTEALKPKAWLEQTREAWADHANRALERAGH 186
                                    11|  |    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181     
                                     12 15                                                                                                                                                                           

Chain A from PDB  Type:PROTEIN  Length:183
 aligned with MOBA2_ECOLX | P07112 from UniProtKB/Swiss-Prot  Length:709

    Alignment length:185
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181     
          MOBA2_ECOLX     2 AIYHLTAKTGSRSGGQSARAKADYIQREGKYARDMDEVLHAESGHMPEFVERPADYWDAADLYERANGRLFKEVEFALPVELTLDQQKALASEFAQHLTGAERLPYTLAIHAGGGENPHCHLMISERINDGIERPAAQWFKRYNGKTPEKGGAQKTEALKPKAWLEQTREAWADHANRALERAGH 186
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------MobA_MobL-2ns6A01 A:17-186                                                                                                                                                 Pfam domains
         Sec.struct. author ....eeeeee.--...hhhhhhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhh......eeeeeee.....hhhhhhhhhhhhhhhhhh.....eeeeeeee...eeeeeeee..........hhhhhh......hhhhh...........hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ns6 A   2 AIYHLTAKTGS--GGQSARAKADYIQREGKYARDMDEVLHAESGHMPEFVERPADYWDAADLYERANGRLFKEVEFALPVELTLDQQKALASEFAQHLTGAERLPYTLAIHAGGGENPHCHLMISERINDGIERPAAQWFKRYNGKTPEKGGAQKTEALKPKAWLEQTREAWADHANRALERAGH 186
                                    11|  |    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181     
                                     12 15                                                                                                                                                                           

   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 2NS6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2NS6)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Rep (10)

(-) Gene Ontology  (12, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MOBA2_ECOLX | P07112)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003916    DNA topoisomerase activity    Catalysis of the transient cleavage and passage of individual DNA strands or double helices through one another, resulting a topological transformation in double-stranded DNA.
    GO:0003917    DNA topoisomerase type I activity    Catalysis of a DNA topological transformation by transiently cleaving one DNA strand at a time to allow passage of another strand; changes the linking number by +1 per catalytic cycle.
    GO:0003899    DNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0032774    RNA biosynthetic process    The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication.
    GO:0000746    conjugation    The union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A   (D0VWX2_PSEAI | D0VWX2)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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