2NRZ - JenaLib

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Asym. Unit - sites (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE C-TERMINAL HALF OF UVRC BOUND TO ITS CATALYTIC DIVALENT CATION

Authors :   E. Karakas, J. J. Truglio, C. Kisker

Date :   02 Nov 06 (Deposition) - 06 Feb 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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, Divalent Cation, Manganese, 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
(for further references see the PDB file header)

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 OF UVRC (RESIDUES 339-557)
	Gene	:	UVRC
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Synonym	:	PROTEIN UVRC, EXCINUCLEASE ABC SUBUNIT C

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	MN	3	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:3 , ASP A:385 , HOH B:195 , ASP B:385	BINDING SITE FOR RESIDUE MN A 301
2	AC2	SOFTWARE	HOH B:49 , HOH B:169 , HOH B:174 , HOH B:196 , ASP B:367 , HIS B:488	BINDING SITE FOR RESIDUE MN B 302
3	AC3	SOFTWARE	HOH A:113 , HOH A:116 , HOH A:186 , HOH A:193 , HOH A:198 , HIS A:488	BINDING SITE FOR RESIDUE MN A 303

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

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

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

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

(no "Exon" information available for 2NRZ)

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:218
 aligned with UVRC_THEMA | Q9WYA3 from UniProtKB/Swiss-Prot  Length:557

    Alignment length:218
                                   349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549        
           UVRC_THEMA   340 RGLRKEALEELMKLLNMKDFPYRIEGIDISHLQGKYTVASLVVFEDGFPKKGDYRRYKIEQDHPDDYESIRTVVKRRYSKHPLPNLLFVDGGIGQVNAAIEALKEIGKDCPVVGLAKKEETVVFENREIHLPHDHPVLRLLVQIRDETHRFAVSYHRKRREKESLRSVLDNVPGIGPIRKKKLIEHFGSLENIRSASLEEIARVIGSTEIARRVLDIL 557
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.......eeeeeeeeee...eeeeeeeeee..ee.hhhheeeeee....hhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhh.....eeee......eee..eee.....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nrz A 340 RGLRKEALEELMKLLNMKDFPYRIEGIDISHLQGKYTVASLVVFEDGFPKKGDYRRYKIEQDHPDDYESIRTVVKRRYSKHPLPNLLFVDGGIGQVNAAIEALKEIGKDCPVVGLAKKEETVVFENREIHLPHDHPVLRLLVQIRDETHRFAVSYHRKRREKESLRSVLDNVPGIGPIRKKKLIEHFGSLENIRSASLEEIARVIGSTEIARRVLDIL 557
                                   349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549

Chain B from PDB  Type:PROTEIN  Length:213
 aligned with UVRC_THEMA | Q9WYA3 from UniProtKB/Swiss-Prot  Length:557

    Alignment length:218
                                                                                                                                                                                                                                                  557 
                                   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-   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------UvrC_HhH_N-2nrzB01 B:350-492                                                                                                                   ------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ---------UvrC_HhH_N-2nrzB02 B:350-492                                                                                                                   ------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhh.......eeeeeeeeeee..eeeeeeeeee..ee.hhhheeeeee....hhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhh.....eeee......eee..eee.....hhhhhhhhhhhhhhhhhhhhh..-----.hhhhhh......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nrz B 341 GLRKEALEELMKLLNMKDFPYRIEGIDISHLQGKYTVASLVVFEDGFPKKGDYRRYKIEQDHPDDYESIRTVVKRRYSKHPLPNLLFVDGGIGQVNAAIEALKEIGKDCPVVGLAKKEETVVFENREIHLPHDHPVLRLLVQIRDETHRFAVSYHR-----ESLRSVLDNVPGIGPIRKKKLIEHFGSLENIRSASLEEIARVIGSTEIARRVLDILG 558
                                   350       360       370       380       390       400       410       420       430       440       450       460       470       480       490     |   - |     510       520       530       540       550        
                                                                                                                                                                                     496   502

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 '\|'

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

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Endonuclease (8)

Family: UvrC_HhH_N (6)

Thermotoga maritima (6)

1a	UvrC_HhH_N-2nrzB01	B:350-492
1b	UvrC_HhH_N-2nrzB02	B:350-492

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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(no "Cis Peptide Bonds" information available for 2nrz)

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

1cyz	THE N TERMINAL ENDONUCLASE DOMAIN OF THE SAME PROTEIN
2nrr	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
2nrx	THE SAME FRAGMENT OF THE PROTEIN CRYSTALLIZED IN DIFFERENT CRYSTAL FORM

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