2IZO - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF AN ARCHAEAL PCNA1-PCNA2-FEN1 COMPLEX

Authors :   A. S. Dore, M. L. Kilkenny, S. M. Roe, L. H. Pearl

Date :   25 Jul 06 (Deposition) - 06 Sep 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Hydrolase, Dna Repair, Dna-Binding, Endonuclease, Metal-Binding, Excision Repair, Dna Replication, Pcna, Fen1, Nuclease, Magnesium (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. S. Dore, M. L. Kilkenny, S. A. Jones, A. W. Oliver, S. M. Roe, S. D. Bell L. H. Pearl
Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex: Elucidating Pcna Subunit And Client Enzyme Specificity.
Nucleic Acids Res. V. 34 4515 2006
PubMed-ID: 16945955 | Reference-DOI: 10.1093/NAR/GKL623

Molecule 1 - FLAP STRUCTURE-SPECIFIC ENDONUCLEASE
	Chains	:	A
	EC Number	:	3.1.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET33B
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 5-349
	Organism Scientific	:	SULFOLOBUS SOLFATARICUS
	Organism Taxid	:	2287
	Synonym	:	FEN1

Molecule 2 - DNA POLYMERASE SLIDING CLAMP C
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P1
	Expression System Taxid	:	562
	Organism Scientific	:	SULFOLOBUS SOLFATARICUS
	Organism Taxid	:	2287
	Synonym	:	PROLIFERATING CELL NUCLEAR ANTIGEN HOMOLOG C, PCNA C, PCNA2

Molecule 3 - DNA POLYMERASE SLIDING CLAMP B
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Taxid	:	562
	Organism Scientific	:	SULFOLOBUS SOLFATARICUS
	Organism Taxid	:	2287
	Synonym	:	PROLIFERATING CELL NUCLEAR ANTIGEN HOMOLOG B, PCNA B, PCNA1

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

No.	Name	Count	Type	Full Name
1	MG	4	Ligand/Ion	MAGNESIUM ION
2	ZN	4	Ligand/Ion	ZINC ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:170 , HOH A:2014	BINDING SITE FOR RESIDUE ZN A1347
2	AC2	SOFTWARE	ASP A:237 , GLU B:146 , ASP B:149	BINDING SITE FOR RESIDUE MG A1348
3	AC3	SOFTWARE	GLU B:61 , LYS B:159 , GLU B:160	BINDING SITE FOR RESIDUE ZN B1246
4	AC4	SOFTWARE	GLU B:234 , GLU C:162 , HOH C:2017 , HOH C:2018	BINDING SITE FOR RESIDUE MG B1247
5	AC5	SOFTWARE	THR C:23 , SER C:25 , ILE C:27 , HIS C:39 , HOH C:2006	BINDING SITE FOR RESIDUE MG C1250
6	AC6	SOFTWARE	GLU C:203 , LYS C:206 , ASP C:207	BINDING SITE FOR RESIDUE ZN C1251
7	AC7	SOFTWARE	GLU C:234 , HIS C:240 , HOH C:2029	BINDING SITE FOR RESIDUE ZN C1252

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

Asymmetric/Biological Unit

No.	Residues
1	Ala A:293	-	Leu A:294
2	Ser B:121	-	Pro B:122
3	Ala B:191	-	Asp B:192
4	Lys C:185	-	Pro C:186

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PCNA_1	PS01251	Proliferating cell nuclear antigen signature 1.	PCNA2_SULSO	33-56	1	B:34-57
2	XPG_1	PS00841	XPG protein signature 1.	FEN_SULSO	73-87	1	A:70-78

(no "Exon" information available for 2IZO)

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:268
 aligned with FEN_SULSO | Q980U8 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:346
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343      
            FEN_SULSO     4 ADLVKDVKRELSFSELKGKRVSIDGYNALYQFLAAIRQPDGTPLMDSQGRVTSHLSGLFYRTINILEEGVIPIYVFDGKPPEQKSEELERRRKAKEEAERKLERAKSEGKIEELRKYSQAILRLSNIMVEESKKLLRAMGIPIVQAPSEGEAEAAYLNKLGLSWAAASQDYDAILFGAKRLVRNLTITGKRKLPNKDVYVEIKPELIETEILLKKLGITREQLIDIGILIGTDYNPDGIRGIGPERALKIIKKYGKIEKAMEYGEISKKDINFNIDEIRGLFLNPQVVKPEEALDLNEPNGEDIINILVYEHNFSEERVKNGIERLTKAIKEAKGASRQTGLDRWF 349
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee.hhhhhh.eeeeeehhhhhhhhhhh....---.........hhhhhhhhhhhhhhhhh.eeeeeee..----------------------------------------------hhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhh....eee...hhhhhh...eeee....-----------......eeeehhhhhhhhh.hhhhhhhhhhhhh...........hhhhhhhhhhhh...-----------------..hhhhhhhh.......-.......hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------XPG_1          ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2izo A   1 MDLVKDVKRELSFSELKGKRVSIDGYNALYQFLAAIRQP---PLMDSQGRVTSHLSGLFYRTINILEEGVIPIYVFDG----------------------------------------------SNIMVEESKKLLRAMGIPIVQAPSEGEAEAAYLNKLGLSWAAASQDYDAILFGAKRLVRNLTI-----------YVEIKPELIETEILLKKLGITREQLIDIGILIGTDYNPDGIRGIGPERALKIIKKYGKI-----------------IDEIRGLFLNPQVVKPE-ALDLNEPNGEDIINILVYEHNFSEERVKNGIERLTKAIKEAKGASRQTGLDRWF 346
                                    10        20        30        |-  |     50        60        70       | -         -         -         -         -    |  130       140       150       160       170       180      |  -       200       210       220       230       240       250      |  -         -    |  280       290| |    300       310       320       330       340      
                                                                 39  43                                 78                                            125                                                           187         199                                                       257               275             291 |                                                     
                                                                                                                                                                                                                                                                                                                              293

Chain B from PDB  Type:PROTEIN  Length:245
 aligned with PCNA2_SULSO | Q97Z84 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:245
                             1                                                                                                                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239     
          PCNA2_SULSO     - -MKAKVIDAVSFSYILRTVGDFLSEANFIVTKEGIRVSGIDPSRVVFLDIFLPSSYFEGFEVSQEKEIIGFKLEDVNDILKRVLKDDTLILSSNESKLTLTFDGEFTRSFELPLIQVESTQPPSVNLEFPFKAQLLTITFADIIDELSDLGEVLNIHSKENKLYFEVIGDLSTAKVELSTDNGTLLEASGADVSSSYGMEYVANTTKMRRASDSMELYFGSQIPLKLRFKLPQEGYGDFYIAPRA 244
               SCOP domains d2izob1 B:1-127 automated matches                                                                                              d2izob2 B:128-245 automated matches                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhhh.eeeeeee..eeeeeee.....eeeeeeee.hhh..eee...eeeeeeehhhhhhhhh......eeeeee...eeeeeee...eeeeeee.................eeeeeehhhhhhhhhh......eeeeee....eeeeee....eeeeee......eeeeee...eeeeehhhhhhhhhhhhh..eeeeeee..eeeeeeeeehhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------PCNA_1  PDB: B:34-57    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2izo B   1 MMKAKVIDAVSFSYILRTVGDFLSEANFIVTKEGIRVSGIDPSRVVFLDIFLPSSYFEGFEVSQEKEIIGFKLEDVNDILKRVLKDDTLILSSNESKLTLTFDGEFTRSFELPLIQVESTSPPSVNLEFPFKAQLLTITFADIIDELSDLGEVLNIHSKENKLYFEVIGDLSTAKVELSTDNGTLLEASGADVSSSYGMEYVANTTKMRRASDSMELYFGSQIPLKLRFKLPQEGYGDFYIAPRA 245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Chain C from PDB  Type:PROTEIN  Length:244
 aligned with PCNA1_SULSO | P57766 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
          PCNA1_SULSO     1 MFKIVYPNAKDFFSFINSITNVTDSIILNFTEDGIFSRHLTEDKVLMAIMRIPKDVLSEYSIDSPTSVKLDVSSVKKILSKASSKKATIELTETDSGLKIIIRDEKSGAKSTIYIKAEKGQVEQLTEPKVNLAVNFTTDESVLNVIAADVTLVGEEMRISTEEDKIKIEAGEEGKRYVAFLMKDKPLKELSIDTSASSSYSAEMFKDAVKGLRGFSAPTMVSFGENLPMKIDVEAVSGGHMIFWIAPRL 249
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhhhhhhhhhhh.....eeee...eeeeeee.....eeeeeeee.hhh.eee....eeeeehhhhhhhhhh...--..eeeeeee..eeeeeee.---..eeeeeeeeeeee............eeeeehhhhhhhhhhhhhhhh.eeeeeee..eeeeeee....eeeeeeee..ee.eeee....eeeeehhhhhhhhhh.......eeeee.....eeeeee.....eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2izo C   1 MFKIVYPNAKDFFSFINSITNVTDSIILNFTEDGIFSRHLTEDKVLMAIMRIPKDVLSEYSIDSPTSVKLDVSSVKKILSKAS--KATIELTETDSGLKIIIRD---GAKSTIYIKAEKGQVEQLTEPKVNLAVNFTTDESVLNVIAADVTLVGEEMRISTEEDKIKIEAGEEGKRYVAFLMKDKPLKELSIDTSASSSYSAEMFKDAVKGLRGFSAPTMVSFGENLPMKIDVEAVSGGHMIFWIAPRL 249
                                    10        20        30        40        50        60        70        80  |  |  90       100   |   110       120       130       140       150       160       170       180       190       200       210       220       230       240         
                                                                                                             83 86               104 108

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: DNA clamp (88)

Superfamily: DNA clamp (88)

Family: automated matches (17)

Protein domain: automated matches (17)

Sulfolobus solfataricus [TaxId: 2287] (4)

1a	d2izob1	B:1-127
1b	d2izob2	B:128-245

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

(no "Pfam Domain" information available for 2IZO)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (FEN_SULSO | Q980U8)

molecular function
	GO:0008409	5'-3' exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end.
	GO:0017108	5'-flap endonuclease activity	Catalysis of the cleavage of a 5' flap structure in DNA, but not other DNA structures; processes the 5' ends of Okazaki fragments in lagging strand DNA synthesis.
	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:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0004527	exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016788	hydrolase activity, acting on ester bonds	Catalysis of the hydrolysis of any ester bond.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	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.
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:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0043137	DNA replication, removal of RNA primer	Removal of the Okazaki RNA primer from the lagging strand of replicating DNA, by a combination of the actions of DNA polymerase, DNA helicase and an endonuclease.
	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.

Chain B (PCNA2_SULSO | Q97Z84)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0030337	DNA polymerase processivity factor activity	An enzyme regulator activity that increases the processivity of polymerization by DNA polymerase, by allowing the polymerase to move rapidly along DNA while remaining topologically bound to it.
biological process
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0006272	leading strand elongation	The synthesis of DNA from a template strand in the 5' to 3' direction; leading strand elongation is continuous as it proceeds in the same direction as the replication fork.
	GO:0006275	regulation of DNA replication	Any process that modulates the frequency, rate or extent of DNA replication.
cellular component
	GO:0043626	PCNA complex	A protein complex composed of three identical PCNA monomers, each comprising two similar domains, which are joined in a head-to-tail arrangement to form a homotrimer. Forms a ring-like structure in solution, with a central hole sufficiently large to accommodate the double helix of DNA. Originally characterized as a DNA sliding clamp for replicative DNA polymerases and as an essential component of the replisome, and has also been shown to be involved in other processes including Okazaki fragment processing, DNA repair, translesion DNA synthesis, DNA methylation, chromatin remodeling and cell cycle regulation.

Chain C (PCNA1_SULSO | P57766)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0030337	DNA polymerase processivity factor activity	An enzyme regulator activity that increases the processivity of polymerization by DNA polymerase, by allowing the polymerase to move rapidly along DNA while remaining topologically bound to it.
biological process
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0006272	leading strand elongation	The synthesis of DNA from a template strand in the 5' to 3' direction; leading strand elongation is continuous as it proceeds in the same direction as the replication fork.
	GO:0006275	regulation of DNA replication	Any process that modulates the frequency, rate or extent of DNA replication.
cellular component
	GO:0043626	PCNA complex	A protein complex composed of three identical PCNA monomers, each comprising two similar domains, which are joined in a head-to-tail arrangement to form a homotrimer. Forms a ring-like structure in solution, with a central hole sufficiently large to accommodate the double helix of DNA. Originally characterized as a DNA sliding clamp for replicative DNA polymerases and as an essential component of the replisome, and has also been shown to be involved in other processes including Okazaki fragment processing, DNA repair, translesion DNA synthesis, DNA methylation, chromatin remodeling and cell cycle regulation.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:293 - Leu A:294	[ RasMol ]
		Ala B:191 - Asp B:192	[ RasMol ]
		Lys C:185 - Pro C:186	[ RasMol ]
		Ser B:121 - Pro B:122	[ RasMol ]

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	2izo
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	FEN_SULSO \| Q980U8
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	PCNA1_SULSO \| P57766
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	PCNA2_SULSO \| Q97Z84
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	3.1.-.-
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	PCNA2_SULSO \| Q97Z84
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UniProtKB/Swiss-Prot
	PCNA1_SULSO \| P57766	:	2hii 2hik 2io4 2ix2 2nti 3fds
	PCNA2_SULSO \| Q97Z84	:	2hii 2hik 2io4 2ix2 2nti 3fds

2ix2	CRYSTAL STRUCTURE OF THE HETEROTRIMERIC PCNA FROM SULFOLOBUS SOLFATARICUS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

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SCOP Domains (1, 2)

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Pfam Domains (0, 0)

Gene Ontology (20, 28)

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Related Entries Specified in the PDB File