3PIH - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   T. MARITIMA UVRA IN COMPLEX WITH FLUORESCEIN-MODIFIED DNA

Authors :   M. Jaciuk, E. Nowak, M. Nowotny

Date :   06 Nov 10 (Deposition) - 19 Jan 11 (Release) - 23 Feb 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym. Unit : A,D
Biol. Unit 1: A,D  (2x)

Keywords :   Hydrolase, Abc Atpase, Dna Repair, Nucleotide Excision Repair, Uvrb, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Jaciuk, E. Nowak, K. Skowronek, A. Tanska, M. Nowotny
Structure Of Uvra Nucleotide Excision Repair Protein In Complex With Modified Dna.
Nat. Struct. Mol. Biol. V. 18 191 2011
PubMed-ID: 21240268 | Reference-DOI: 10.1038/NSMB.1973

Molecule 1 - UVRABC SYSTEM PROTEIN A
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	UVRA, TM_0480
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Synonym	:	UVRA PROTEIN, EXCINUCLEASE ABC SUBUNIT A

Molecule 2 - DNA (32-MER)
	Chains	:	D
	Engineered	:	YES
	Other Details	:	SYNTHETIC DNA OLIGO
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	PPV	2	Ligand/Ion	PYROPHOSPHATE
2	ZN	3	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	PPV	4	Ligand/Ion	PYROPHOSPHATE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:469 , SER A:619 , GLY A:620 , SER A:621 , GLY A:622 , LYS A:623 , SER A:624	BINDING SITE FOR RESIDUE PPV A 1001
2	AC2	SOFTWARE	SER A:33 , GLY A:34 , SER A:35 , GLY A:36 , LYS A:37 , SER A:38 , HIS A:524 , SER A:807 , GLY A:809 , GLY A:838	BINDING SITE FOR RESIDUE PPV A 1002
3	AC3	SOFTWARE	CYS A:716 , CYS A:719 , CYS A:739 , CYS A:742	BINDING SITE FOR RESIDUE ZN A 917
4	AC4	SOFTWARE	CYS A:276 , CYS A:279 , CYS A:384 , CYS A:387	BINDING SITE FOR RESIDUE ZN A 918
5	AC5	SOFTWARE	CYS A:120 , CYS A:123 , CYS A:252 , CYS A:255	BINDING SITE FOR RESIDUE ZN A 919

(no "SS Bond" information available for 3PIH)

Asymmetric Unit

No.	Residues
1	Ser A:328	-	Pro A:329
2	Glu A:369	-	Met A:370
3	Gly A:539	-	Pro A:540
4	Gly A:881	-	Pro A:882

(no "SAP(SNP)/Variant" information available for 3PIH)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ABC_TRANSPORTER_1	PS00211	ABC transporters family signature.	UVRA_THEMA	465-479 806-820	2	A:465-479 A:806-820

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ABC_TRANSPORTER_1	PS00211	ABC transporters family signature.	UVRA_THEMA	465-479 806-820	4	A:465-479 A:806-820

(no "Exon" information available for 3PIH)

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:836
 aligned with UVRA_THEMA | Q9WYV0 from UniProtKB/Swiss-Prot  Length:916

    Alignment length:915
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911     
           UVRA_THEMA     2 NEIVVKGARVHNLKNITVRIPKNRLVVITGVSGSGKSSLAMDTIYAEGQRRYLESLSTYARQFLGNLKKPDVDEIEGLSPAIAIDQKTVSHNPRSTVGTVTEIYDYLRVLYARIGKAHCPECGRPLEKKSIDEILQDLFNSFKEGSRIYILAPVATEKKGTFKKEIEEFISKGFARIEIDGEIYRLEEVPELDKNKRHTVKLVVDRLILETRNEHRILDSLELAMREGKGFVEIRNVDTGESKIFSENLMCPVCGIGFPEITPKLFSFNSPYGACPNCHGLGFTFEVDPSLVIDEEKSVLEGAIIPYRWDRRLSRWVAREIEKRGVSPHLPFKDLPEDVKEFILYGDDRFEGVVPKVQRWHRETESPEMKEWLEKNFIVQRTCSVCGGRRLNREALSVKINGLNIHEFTELSISEELEFLKNLNLTEREREIVGELLKEIEKRLEFLVDVGLEYLTLSRSATTLSGGESQRIRLATQIGSGLTGVIYVLDEPTIGLHPRDTERLIKTLKKLRDLGNTVIVVEHDEEVIRNADHIIDIGPGGGTNGGRVVFQGTVDELLKNPDSSLTGEYLSGKRKITVNKTRRLPYASLKIKGVRHNNLKNIDVEIPLGVFVCVTGVSGSGKSSLVMETLYPALMNLLHKTKLPAGEFDSIEGHENIDKMIAIDQSPIGRTPRSNPATYTKVFDEIRSLFAMTPAAKARGYNKSRFSFNLKGGRCEACQGQGYVKIEMLFLPDVYVECDVCKGKRYNRETLEITYKGKNISDILDMTVDEALEFFKNIPSIKRTLQVLHDVGLGYVKLGQPATTLSGGEAQRIKLASELRKRDTGRTLYILDEPTVGLHFEDVRKLVEVLHRLVDRGNTVIVIEHNLDVIKNADHIIDLGPEGGKEGGYIVATGTPEEIAKNPHSYTGRFLKNVL 916
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ABC_tran-3pihA01 A:630-837                                                                                                                                                                                      ------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ABC_tran-3pihA02 A:630-837                                                                                                                                                                                      ------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeee............eee...eeeeee.....hhhhhh.hhhhhhhhhhhh.....--------......eee....eeee....-......hhhhhhhhhhhhhhhhhhh.ee............hhhhhhhhhhhhh....eeeee..------------------------------------------------...eeee.hhhhhhhhhhhhhhhhhhhh.eeeeee.....eeeee...............hhhhhh...............eeeee.....----------.hhhhh.hhhhhhhhhhhhh......-------....hhhhhhh.--..hhhhhhhhhhhh.---.hhhhhhhh.eeeee...........hhh.eee..eehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhh.....eeeee......hhhhhhhhhhhhhhh.....eeeee..hhhhhhh..eeeeee..hhhhh.eeeeeehhhhhhhh...hhhhhhhhh...............eeeeeee.......eeeeee...eeeee.....hhhhhhhhhhhhhhhhhhhh.........eeehhhhh.eeeee...........hhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhh...............eeee.......eeee...........hhhhh.....hhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh......eeeeee......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhh...eeeeee..hhhhh.eeeeeehhhhhhh...hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ABC_TRANSPORTER--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ABC_TRANSPORTER------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pih A   2 NEIVVKGARVHNLKNITVRIPKNRLVVITGVSGSGKSSLAMDTIYAEGQRRYLESLSTY--------KKPDVDEIEGLSPAIAIDQKT-SHNPRSTVGTVTEIYDYLRVLYARIGKAHCPECGRPLEKKSIDEILQDLFNSFKEGSRIYILAP------------------------------------------------LVVDRLILETRNEHRILDSLELAMREGKGFVEIRNVDTGESKIFSENLMCPVCGIGFPEITPKLFSFNSPYGACPNCHGLGFTFEVDPSLV----------AIIPYRWDRRLSRWVAREIEKRGVSP-------PEDVKEFILYGD--FEGVVPKVQRWHRET---EMKEWLEKNFIVQRTCSVCGGRRLNREALSVKINGLNIHEFTELSISEELEFLKNLNLTEREREIVGELLKEIEKRLEFLVDVGLEYLTLSRSATTLSGGESQRIRLATQIGSGLTGVIYVLDEPTIGLHPRDTERLIKTLKKLRDLGNTVIVVEHDEEVIRNADHIIDIGPGGGTNGGRVVFQGTVDELLKNPDSSLTGEYLSGKRKITVNKTRRLPYASLKIKGVRHNNLKNIDVEIPLGVFVCVTGVSGSGKSSLVMETLYPALMNLLHKTKLPAGEFDSIEGHENIDKMIAIDQSPIGRTPRSNPATYTKVFDEIRSLFAMTPAAKARGYNKSRFSFNLKGGRCEACQGQGYVKIEMLFLPDVYVECDVCKGKRYNRETLEITYKGKNISDILDMTVDEALEFFKNIPSIKRTLQVLHDVGLGYVKLGQPATTLSGGEAQRIKLASELRKRDTGRTLYILDEPTVGLHFEDVRKLVEVLHRLVDRGNTVIVIEHNLDVIKNADHIIDLGPEGGKEGGYIVATGTPEEIAKNPHSYTGRFLKNVL 916
                                    11        21        31        41        51        |-       |71        81       |91       101       111       121       131       141       151  |      -         -         -         -         - |     211       221       231       241       251       261       271       281       291 |       -  |    311       321       | -     | 341      |351       361   |   371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911     
                                                                                     60       69                  89 |                                                            154                                              203                                                                                       293        304                      329     337        348  |           365 369                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
                                                                                                                    91                                                                                                                                                                                                                                                                 351

Chain D from PDB  Type:DNA  Length:32
                                                                
                 3pih D   1 AGTGATCAGTGGTTCCGGAACCACTGATCACT  32
                                    10        20        30

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 3PIH)

(no "CATH Domain" information available for 3PIH)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: ABC_tran (53)

Thermotoga maritima (4)

1a	ABC_tran-3pihA01	A:630-837
1b	ABC_tran-3pihA02	A:630-837

Asymmetric Unit(hide GO term definitions)

Chain A (UVRA_THEMA | Q9WYV0)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016887	ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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: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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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 Unit
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	Cis Peptide Bonds
		Glu A:369 - Met A:370	[ RasMol ]
		Gly A:539 - Pro A:540	[ RasMol ]
		Gly A:881 - Pro A:882	[ RasMol ]
		Ser A:328 - Pro A:329	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

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