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Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE GIY-YIG N-TERMINAL ENDONUCLEASE DOMAIN OF UVRC FROM THERMOTOGA MARITIMA: POINT MUTANT N88A BOUND TO ITS CATALYTIC DIVALENT CATION

Authors :   J. J. Truglio, B. Rhau, D. L. Croteau, L. Wang, M. Skorvaga, E. Karakas, M. J. Dellavecchia, H. Wang, B. Van Houten, C. Kisker

Date :   23 Dec 04 (Deposition) - 01 Mar 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A

Keywords :   Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. J. Truglio, B. Rhau, D. L. Croteau, L. Wang, M. Skorvaga, E. Karakas, M. J. Dellavecchia, H. Wang, B. Van Houten, C. Kisker
Structural Insights Into The First Incision Reaction During Nucleotide Excision Repair
Embo J. V. 24 885 2005
PubMed-ID: 15692561 | Reference-DOI: 10.1038/SJ.EMBOJ.7600568

Molecule 1 - UVRABC SYSTEM PROTEIN C
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	N-TERMINAL DOMAIN
	Mutation	:	YES
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Synonym	:	UVRC PROTEIN, EXCINUCLEASE ABC SUBUNIT C

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 3)

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

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:76 , HOH A:1069 , HOH A:1079 , HOH A:1084 , HOH A:1085 , HOH A:1086	BINDING SITE FOR RESIDUE MN A 1001
2	AC2	SOFTWARE	MET A:1 , ARG A:6 , ASN A:68 , HOH A:1050	BINDING SITE FOR RESIDUE MN A 1002
3	AC3	SOFTWARE	GLU A:60	BINDING SITE FOR RESIDUE MN A 1004

(no "SS Bond" information available for 1YD5)

(no "Cis Peptide Bond" information available for 1YD5)

(no "SAP(SNP)/Variant" information available for 1YD5)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GIY_YIG	PS50164	GIY-YIG domain profile.	UVRC_THEMA	14-89	1	A:14-89

(no "Exon" information available for 1YD5)

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
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Chain A from PDB  Type:PROTEIN  Length:90
 aligned with UVRC_THEMA | Q9WYA3 from UniProtKB/Swiss-Prot  Length:557

    Alignment length:90
                                    10        20        30        40        50        60        70        80        90
            UVRC_THEMA    1 MKEKIRKKILLAPEEPGVYIFKNKGVPIYIGKAKRLSNRLRSYLNPQTEKVFRIGEEADELETIVVMNEREAFILEANLIKKYRPKYNVR 90
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh....eeeeeee..eeeeeeee.hhhhhhhhhhh..hhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------GIY_YIG  PDB: A:14-89 UniProt: 14-89                                        - PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                  1yd5 A  1 MKEKIRKKILLAPEEPGVYIFKNKGVPIYIGKAKRLSNRLRSYLNPQTEKVFRIGEEADELETIVVMNEREAFILEANLIKKYRPKYAVR 90
                                    10        20        30        40        50        60        70        80        90

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 1YD5)

(no "CATH Domain" information available for 1YD5)

(no "Pfam Domain" information available for 1YD5)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1yd5)

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

1d9x	CRYSTAL STRUCTURE OF UVRB
1kft	SOLUTION STRUCTURE OF THE C-TERMINAL DOMAIN OF UVRC FROM E- COLI
1ln0	ENDONUCLEASE DOMAIN OF I-TEVI
1mk0	ENDONUCLEASE DOMAIN OF I-TEVI
1ycz	THE SAME PROTEIN FROM THERMOTOGA MARITIMA
1yd0	THE SAME PROTEIN FROM THERMOTOGA MARITIMA BOUND TO MANGANESE
1yd1	THE SAME PROTEIN FROM THERMOTOGA MARITIMA BOUND TO MAGNESIUM
1yd2	THE SAME PROTEIN FROM THERMOTOGA MARITIMA Y19F MUTANT BOUND TO MANGANESE
1yd3	THE SAME PROTEIN FROM THERMOTOGA MARITIMA Y43F MUTANT BOUND TO MANGANESE
1yd4	THE SAME PROTEIN FROM THERMOTOGA MARITIMA Y29F MUTANT BOUND TO MANGANESE
1yd6	THE SAME PROTEIN FROM BACILLUS CALDOTENAX

Description

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Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

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