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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL HALF OF UVRC, IN THE PRESENCE OF SULFATE MOLECULES
 
Authors :  E. Karakas, J. J. Truglio, C. Kisker
Date :  02 Nov 06  (Deposition) - 06 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Uvrc, Rnase H, Endonuclase, Helix Hairpin Helix, Uvrabc, Ner, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Karakas, J. J. Truglio, D. Croteau, B. Rhau, L. Wang, B. Van Houten, C. Kisker
Structure Of The C-Terminal Half Of Uvrc Reveals An Rnase H Endonuclease Domain With An Argonaute-Like Catalytic Triad.
Embo J. V. 26 613 2007
PubMed-ID: 17245438  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601497

(-) Compounds

Molecule 1 - UVRABC SYSTEM PROTEIN C
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTXB1
    Expression System Strain: BL21-CODONPLUS (CE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: THE RNASE H ENDONUCLASE AND HELIX HAIRPIN HELIX DOMAINS (RESIDUES 339-557)
    Gene: UVRC
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: PROTEIN UVRC, EXCINUCLEASE ABC SUBUNIT C

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO48Ligand/IonSULFATE ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:514 , GLY A:515 , PRO A:516 , ILE A:517 , ARG A:518BINDING SITE FOR RESIDUE SO4 A 901
2AC2SOFTWAREHOH A:75 , HOH A:83 , ARG A:395 , GLU A:459 , LEU A:470 , PRO A:471 , HIS A:472 , SER A:493 , TYR A:494BINDING SITE FOR RESIDUE SO4 A 902
3AC3SOFTWAREHOH A:56 , TYR A:406 , GLY A:431 , ILE A:432 , GLY A:433 , GLN A:434BINDING SITE FOR RESIDUE SO4 A 903
4AC4SOFTWAREHOH A:9 , HOH A:50 , HOH A:135 , HOH A:297 , ARG A:394 , TYR A:396 , LYS A:419 , HIS A:420 , ARG A:466 , ILE A:468BINDING SITE FOR RESIDUE SO4 A 904
5AC5SOFTWAREGLY B:515 , PRO B:516 , ILE B:517 , ARG B:518BINDING SITE FOR RESIDUE SO4 B 901
6AC6SOFTWAREARG B:395 , HIS B:472BINDING SITE FOR RESIDUE SO4 B 902
7AC7SOFTWARETYR B:406 , GLY B:431 , GLY B:433 , GLN B:434BINDING SITE FOR RESIDUE SO4 B 903
8AC8SOFTWAREHOH B:27 , HOH B:51 , ARG B:394 , TYR B:396 , ARG B:415 , LYS B:419 , HIS B:420 , ILE B:468BINDING SITE FOR RESIDUE SO4 B 904
9AC9SOFTWAREARG A:362 , ASP A:392 , ARG A:394 , ARG A:416 , HIS A:420BINDING SITE FOR RESIDUE GOL A 905

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2NRX)

(-) 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:217
 aligned with UVRC_THEMA | Q9WYA3 from UniProtKB/Swiss-Prot  Length:557

    Alignment length:217
                                   350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       
           UVRC_THEMA   341 GLRKEALEELMKLLNMKDFPYRIEGIDISHLQGKYTVASLVVFEDGFPKKGDYRRYKIEQDHPDDYESIRTVVKRRYSKHPLPNLLFVDGGIGQVNAAIEALKEIGKDCPVVGLAKKEETVVFENREIHLPHDHPVLRLLVQIRDETHRFAVSYHRKRREKESLRSVLDNVPGIGPIRKKKLIEHFGSLENIRSASLEEIARVIGSTEIARRVLDIL 557
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.......eeeeeeeeee...eeeeeeeeee..ee.hhhheeeeee....hhhhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhhh.....eeee.....eeee..eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nrx A 341 GLRKEALEELMKLLNMKDFPYRIEGIDISHLQGKYTVASLVVFEDGFPKKGDYRRYKIEQDHPDDYESIRTVVKRRYSKHPLPNLLFVDGGIGQVNAAIEALKEIGKDCPVVGLAKKEETVVFENREIHLPHDHPVLRLLVQIRDETHRFAVSYHRKRREKESLRSVLDNVPGIGPIRKKKLIEHFGSLENIRSASLEEIARVIGSTEIARRVLDIL 557
                                   350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       


Chain B from PDB  Type:PROTEIN  Length:208
 aligned with UVRC_THEMA | Q9WYA3 from UniProtKB/Swiss-Prot  Length:557

    Alignment length:216
                                   351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551      
           UVRC_THEMA   342 LRKEALEELMKLLNMKDFPYRIEGIDISHLQGKYTVASLVVFEDGFPKKGDYRRYKIEQDHPDDYESIRTVVKRRYSKHPLPNLLFVDGGIGQVNAAIEALKEIGKDCPVVGLAKKEETVVFENREIHLPHDHPVLRLLVQIRDETHRFAVSYHRKRREKESLRSVLDNVPGIGPIRKKKLIEHFGSLENIRSASLEEIARVIGSTEIARRVLDIL 557
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --------UvrC_HhH_N-2nrxB01 B:350-492                                                                                                                   ----      ------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------UvrC_HhH_N-2nrxB02 B:350-492                                                                                                                   ----      ------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhh.......eeeeeeeeee...eeeeeeeeee..ee.hhhheeeeee....hhhhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhhh.....eeeee--..eeee..eee.....hhhhhhhhhhhhhhhhhhhhh..------hhhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nrx B 342 LRKEALEELMKLLNMKDFPYRIEGIDISHLQGKYTVASLVVFEDGFPKKGDYRRYKIEQDHPDDYESIRTVVKRRYSKHPLPNLLFVDGGIGQVNAAIEALKEIGKDCPVVGLA--EETVVFENREIHLPHDHPVLRLLVQIRDETHRFAVSYHR------SLRSVLDNVPGIGPIRKKKLIEHFGSLENIRSASLEEIARVIGSTEIARRVLDIL 557
                                   351       361       371       381       391       401       411       421       431       441       451   |  |461       471       481       491    |    - |     511       521       531       541       551      
                                                                                                                                           455  |                                   496    503                                                      
                                                                                                                                              458
   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 2NRX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Endonuclease (8)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (UVRC_THEMA | Q9WYA3)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0009381    excinuclease ABC activity    Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid at sites flanking regions of damaged DNA to which the Uvr ABC excinuclease complexes bind.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
    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:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006289    nucleotide-excision repair    A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0009380    excinuclease repair complex    Any of the protein complexes formed by the UvrABC excinuclease system, which carries out nucleotide excision repair. Three different complexes are formed by the 3 proteins as they proceed through the excision repair process. First a complex consisting of two A subunits and two B subunits bind DNA and unwind it around the damaged site. Then, the A subunits disassociate leaving behind a stable complex between B subunits and DNA. Now, subunit C binds to this B+DNA complex and causes subunit B to nick the DNA on one side of the complex while subunit C nicks the DNA on the other side of the complex. DNA polymerase I and DNA ligase can then repair the resulting gap.

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 Related Entries

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

UniProtKB/Swiss-Prot
        UVRC_THEMA | Q9WYA3: 1ycz 1yd0 1yd1 1yd2 1yd3 1yd4 1yd5 2nrr 2nrt 2nrv 2nrw 2nrz

(-) Related Entries Specified in the PDB File

1ycz THE N TERMINAL ENDONUCLASE DOMAIN OF THE SAME PROTEIN
2nrr THE RNASEH ENDONUCLASE DOMAIN OF THE SAME PROTEIN
2nrt THE SAME FRAGMENT OF THE PROTEIN CRYSTALLIZED IN DIFFERENT CRYSTAL FORM
2nrv THE SAME FRAGMENT OF THE PROTEIN CRYSTALLIZED IN DIFFERENT CRYSTAL FORM
2nrw THE SAME FRAGMENT OF THE PROTEIN CRYSTALLIZED IN DIFFERENT CRYSTAL FORM
2nrz