3V61 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF S. CEREVISIAE PCNA CONJUGATED TO SUMO ON LYSINE 164

Authors :   A. A. Armstrong, F. Mohideen, C. D. Lima

Date :   18 Dec 11 (Deposition) - 29 Feb 12 (Release) - 18 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Ubiquitin-Like Protein Pcna, Post-Translational Modification, Dna Replication, Dna Damage Response, Srs2, Nem Modification On Pcna Cys22 And Cys81, Nuclear, Protein Binding-Dna Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. A. Armstrong, F. Mohideen, C. D. Lima
Recognition Of Sumo-Modified Pcna Requires Tandem Receptor Motifs In Srs2.
Nature V. 483 59 2012
PubMed-ID: 22382979 | Reference-DOI: 10.1038/NATURE10883

Molecule 1 - UBIQUITIN-LIKE PROTEIN SMT3
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3) PLYSS
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 20-98
	Gene	:	D9719.15, SMT3, YDR510W
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	W3031A

Molecule 2 - PROLIFERATING CELL NUCLEAR ANTIGEN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21B
	Expression System Strain	:	BL21(DE3)CP RIL
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	POL30, YBR0811, YBR088C
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	W3031A
	Synonym	:	PCNA

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 15)

No.	Name	Count	Type	Full Name
1	BA	13	Ligand/Ion	BARIUM ION
2	NEQ	2	Ligand/Ion	N-ETHYLMALEIMIDE

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH A:6 , ASP A:82 , ASP A:85 , HOH A:100	BINDING SITE FOR RESIDUE BA A 2
02	AC2	SOFTWARE	ASP A:87	BINDING SITE FOR RESIDUE BA A 3
03	AC3	SOFTWARE	HIS A:23 , ASP A:82 , ASP A:85	BINDING SITE FOR RESIDUE BA A 4
04	AC4	SOFTWARE	HOH A:113 , ASP B:33	BINDING SITE FOR RESIDUE BA A 11
05	AC5	SOFTWARE	ASP B:21 , ASP B:214 , HOH B:275 , HOH B:280 , HOH B:323	BINDING SITE FOR RESIDUE BA B 259
06	AC6	SOFTWARE	ASP B:240 , LEU B:241 , HOH B:270 , HOH B:273 , HOH B:322	BINDING SITE FOR RESIDUE BA B 260
07	AC7	SOFTWARE	PHE B:57 , BA B:262 , HOH B:299	BINDING SITE FOR RESIDUE BA B 261
08	AC8	SOFTWARE	GLU B:55 , BA B:261	BINDING SITE FOR RESIDUE BA B 262
09	AC9	SOFTWARE	GLU B:7 , THR B:85 , THR B:87	BINDING SITE FOR RESIDUE BA B 263
10	BC1	SOFTWARE	ASP B:93 , ASN B:94 , THR B:95 , HOH B:340	BINDING SITE FOR RESIDUE BA B 264
11	BC2	SOFTWARE	HOH A:108 , HOH B:293	BINDING SITE FOR RESIDUE BA B 265
12	BC3	SOFTWARE	ASP B:172	BINDING SITE FOR RESIDUE BA B 266
13	BC4	SOFTWARE	ARG B:80 , GLY B:82 , HOH B:274 , HOH B:276	BINDING SITE FOR RESIDUE BA B 267
14	BC5	SOFTWARE	GLY B:18 , PHE B:19 , CYS B:22 , VAL B:48 , ASP B:214	BINDING SITE FOR RESIDUE NEQ B 268
15	BC6	SOFTWARE	ILE B:78 , CYS B:81 , ASP B:150 , GLN B:153 , LEU B:154 , HOH B:324	BINDING SITE FOR RESIDUE NEQ B 269

(no "SS Bond" information available for 3V61)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:97	-	Gly A:98

(no "SAP(SNP)/Variant" information available for 3V61)

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_2	PS50053	Ubiquitin domain profile.	SMT3_YEAST	22-98	1	A:22-98
2	PCNA_1	PS01251	Proliferating cell nuclear antigen signature 1.	PCNA_YEAST	34-57	1	B:34-57
3	PCNA_2	PS00293	Proliferating cell nuclear antigen signature 2.	PCNA_YEAST	61-79	1	B:61-79

Asymmetric/Biological Unit (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YBR088C	1	YBR088C.1	II:425760-424984	777	PCNA_YEAST	1-258	258	1	B:1-254	254

2.1	YDR510W	1	YDR510W.1	IV:1469393-1469698	306	SMT3_YEAST	1-101	101	1	A:22-98	77

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:77
 aligned with SMT3_YEAST | Q12306 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:77
                                    31        41        51        61        71        81        91       
           SMT3_YEAST    22 THINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGG  98
               SCOP domains d3v61a_ A: automated matches                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eeeee......hhhhhhhhhhh...hhh.eeeee..ee.....hhhhhh.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE UBIQUITIN_2  PDB: A:22-98 UniProt: 22-98                                      PROSITE
               Transcript 2 Exon 2.1  PDB: A:22-98 UniProt: 1-101 [INCOMPLETE]                            Transcript 2
                 3v61 A  22 THINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGG  98
                                    31        41        51        61        71        81        91

Chain B from PDB  Type:PROTEIN  Length:254
 aligned with PCNA_YEAST | P15873 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:254
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250    
           PCNA_YEAST     1 MLEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIGVEAFQEYRCDHPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEYSLKLMDIDADFLKIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMITKETIKFVADGDIGSGSVIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKSGFLQFFLAPKF 254
               SCOP domains d3v61b1 B:1-126 automated matches                                                                                             d3v61b2 B:127-254 automated matches                                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhhh.eeeeeee..eeeeeee.....eeeeeeee.hhh.eeee...eeeeeehhhhhhhhhhh....eeeeee.....eeeeeee.hhhh.eeeeeee.................eeeeeehhhhhhhhhhhhh...eeeeeee..eeeeeee....eeeeee.......hhhhh.eeee...eeeeeehhhhhhhhhhhhh..eeeeee.....eeeeee...eeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------PCNA_1  PDB: B:34-57    ---PCNA_2  PDB: B:61-7------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: B:1-254 UniProt: 1-258 [INCOMPLETE]                                                                                                                                                                                                             Transcript 1
                 3v61 B   1 MLEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIGVEAFQEYRCDHPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEYSLKLMDIDADFLGIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMITKETIKFVADGDIGSGSVIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKSGFLQFFLAPKF 254
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250

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: beta-Grasp (ubiquitin-like) (1032)

Superfamily: Ubiquitin-like (546)

Family: Ubiquitin-related (337)

Protein domain: automated matches (80)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 559292] (3)

d3v61a_

Fold: DNA clamp (88)

Superfamily: DNA clamp (88)

Family: DNA polymerase processivity factor (40)

Protein domain: automated matches (10)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 559292] (4)

2a	d3v61b1	B:1-126
2b	d3v61b2	B:127-254

(no "CATH Domain" information available for 3V61)

(no "Pfam Domain" information available for 3V61)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SMT3_YEAST | Q12306)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0031386	protein tag	A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation.
biological process
	GO:0000070	mitotic sister chromatid segregation	The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets.
	GO:0016925	protein sumoylation	The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
cellular component
	GO:0000794	condensed nuclear chromosome	A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005940	septin ring	A tight ring-shaped structure that forms in the division plane at the site of cytokinesis; composed of members of the conserved family of filament-forming proteins called septins as well as septin-associated proteins. This type of septin structure is observed at the bud neck of budding fungal cells, at the site of cell division in animal cells, at the junction between the mother cell and a pseudohyphal projection, and also within hyphae of filamentous fungi at sites where a septum will form.

Chain B (PCNA_YEAST | P15873)

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.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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: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:0030466	chromatin silencing at silent mating-type cassette	Repression of transcription at silent mating-type loci by alteration of the structure of chromatin.
	GO:0006348	chromatin silencing at telomere	Repression of transcription of telomeric DNA by altering the structure of chromatin.
	GO:0070987	error-free translesion synthesis	The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions but does not causes an increase in the endogenous mutation level. For S. cerevisiae, RAD30 encodes DNA polymerase eta, which incorporates two adenines. When incorporated across a thymine-thymine dimer, it does not increase the endogenous mutation level.
	GO:0034087	establishment of mitotic sister chromatid cohesion	The process in which the sister chromatids of a replicated chromosome become joined along the entire length of the chromosome during S phase during a mitotic cell cycle.
	GO:0006273	lagging strand elongation	The synthesis of DNA from a template strand in a net 3' to 5' direction. Lagging strand DNA elongation proceeds by discontinuous synthesis of short stretches of DNA, known as Okazaki fragments, from RNA primers; these fragments are then joined by DNA ligase. Although each segment of nascent DNA is synthesized in the 5' to 3' direction, the overall direction of lagging strand synthesis is 3' to 5', mirroring the progress of the replication fork.
	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:0035753	maintenance of DNA trinucleotide repeats	Any process involved in sustaining the fidelity and copy number of DNA trinucleotide repeats. DNA trinucleotide repeats are naturally occurring runs of three base-pairs.
	GO:0000710	meiotic mismatch repair	A system for the identification and correction of base-base mismatches, small insertion-deletion loops, and regions of heterology that are present in duplex DNA formed with strands from two recombining molecules. Correction of the mismatch can result in non-Mendelian segregation of alleles following meiosis.
	GO:0006298	mismatch repair	A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.
	GO:0000278	mitotic cell cycle	Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
	GO:0007064	mitotic sister chromatid cohesion	The cell cycle process in which the sister chromatids of a replicated chromosome are joined along the entire length of the chromosome, from their formation in S phase through metaphase during a mitotic cell cycle. This cohesion cycle is critical for high fidelity chromosome transmission.
	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).
	GO:1902394	positive regulation of exodeoxyribonuclease activity	Any process that activates or increases the frequency, rate or extent of exodeoxyribonuclease activity.
	GO:1903022	positive regulation of phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands	Any process that activates or increases the frequency, rate or extent of phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands.
	GO:0006301	postreplication repair	The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication. Includes pathways that remove replication-blocking lesions in conjunction with DNA replication.
	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.
	GO:0000781	chromosome, telomeric region	The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005657	replication fork	The Y-shaped region of a replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:97 - Gly A:98	[ RasMol ]

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	3v61
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	SMT3_YEAST \| Q12306
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 15)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (2, 2)

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SCOP Domains (2, 3)

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Gene Ontology (32, 35)

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