3H4L - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF N TERMINAL DOMAIN OF A DNA REPAIR PROTEIN

Authors :   M. E. Arana, S. F. Holmes, J. M. Fortune, A. F. Moon, L. C. Pedersen, T. A. K

Date :   20 Apr 09 (Deposition) - 02 Mar 10 (Release) - 28 Apr 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)

Keywords :   Pms1, Atp Binding, Dna Repair, Dna Damage, Nucleus, Phosphoprotein, Dna Binding Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. E. Arana, S. F. Holmes, J. M. Fortune, A. F. Moon, L. C. Pedersen, T. A. Kunkel
Functional Residues On The Surface Of The N-Terminal Domain Of Yeast Pms1.
Dna Repair V. 9 448 2010
PubMed-ID: 20138591 | Reference-DOI: 10.1016/J.DNAREP.2010.01.010

Molecule 1 - DNA MISMATCH REPAIR PROTEIN PMS1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX4T3
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 1-365
	Gene	:	PMS1
	Organism Common	:	BREWER'S YEAST,LAGER BEER YEAST,YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	POSTMEIOTIC SEGREGATION PROTEIN 1

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:	A
Biological Unit 3 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	ANP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	ANP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:1 , HOH A:2 , ASN A:65 , ALA A:69 , ASP A:90 , GLY A:94 , ILE A:95 , LEU A:103 , GLY A:125 , PHE A:126 , ARG A:127 , GLY A:128 , ALA A:130 , LEU A:131 , THR A:174 , LYS A:364 , HOH A:398 , HOH A:399 , HOH A:420 , HOH A:439 , MG A:701 , LYS B:229 , ASN B:231	BINDING SITE FOR RESIDUE ANP A 397
2	AC2	SOFTWARE	HOH A:1 , HOH A:2 , ASN A:65 , ANP A:397	BINDING SITE FOR RESIDUE MG A 701
3	AC3	SOFTWARE	HOH B:3 , HOH B:4 , HOH B:5 , HOH B:6 , HOH B:21 , HOH B:29 , ASN B:65 , ALA B:69 , ASP B:90 , ILE B:95 , LEU B:103 , ARG B:127 , GLY B:128 , ALA B:130 , LEU B:131 , THR B:174 , HOH B:399 , HOH B:408 , HOH B:423 , MG B:702	BINDING SITE FOR RESIDUE ANP B 397
4	AC4	SOFTWARE	HOH B:3 , HOH B:4 , ASN B:65 , ANP B:397	BINDING SITE FOR RESIDUE MG B 702

(no "SS Bond" information available for 3H4L)

Asymmetric Unit

No.	Residues
1	Pro A:148	-	Pro A:149
2	Pro B:148	-	Pro B:149

Asymmetric Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PMS1_YEAST_001 *	N	41	S	PMS1_YEAST	---	---	A/B	N	72	S
2	UniProt	VAR_PMS1_YEAST_002 *	I	112	T	PMS1_YEAST	---	---	A/B	I	143	T
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PMS1_YEAST_001 *	N	41	S	PMS1_YEAST	---	---	A/B	N	72	S
2	UniProt	VAR_PMS1_YEAST_002 *	I	112	T	PMS1_YEAST	---	---	A/B	I	143	T
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PMS1_YEAST_001 *	N	41	S	PMS1_YEAST	---	---	A	N	72	S
2	UniProt	VAR_PMS1_YEAST_002 *	I	112	T	PMS1_YEAST	---	---	A	I	143	T
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PMS1_YEAST_001 *	N	41	S	PMS1_YEAST	---	---	B	N	72	S
2	UniProt	VAR_PMS1_YEAST_002 *	I	112	T	PMS1_YEAST	---	---	B	I	143	T
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_MISMATCH_REPAIR_1	PS00058	DNA mismatch repair proteins mutL / hexB / PMS1 signature.	PMS1_YEAST	94-100	2	A:125-131 B:125-131

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_MISMATCH_REPAIR_1	PS00058	DNA mismatch repair proteins mutL / hexB / PMS1 signature.	PMS1_YEAST	94-100	2	A:125-131 B:125-131

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_MISMATCH_REPAIR_1	PS00058	DNA mismatch repair proteins mutL / hexB / PMS1 signature.	PMS1_YEAST	94-100	1	A:125-131 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_MISMATCH_REPAIR_1	PS00058	DNA mismatch repair proteins mutL / hexB / PMS1 signature.	PMS1_YEAST	94-100	1	- B:125-131

(no "Exon" information available for 3H4L)

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:333
 aligned with PMS1_YEAST | P14242 from UniProtKB/Swiss-Prot  Length:873

    Alignment length:354
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360    
           PMS1_YEAST    11 DVHRITSGQVITDLTTAVKELVDNSIDANANQIEIIFKDYGLESIECSDNGDGIDPSNYEFLALKHYTSKIAKFQDVAKVQTLGFRGEALSSLCGIAKLSVITTTSPPKADKLEYDMVGHITSKTTTSRNKGTTVLVSQLFHNLPVRQKEFSKTFKRQFTKCLTVIQGYAIINAAIKFSVWNITPKGKKNLILSTMRNSSMRKNISSVFGAGGMRGLEEVDLVLDLNPFKNRMLGKYTDDPDFLDLDYKIRVKGYISQNSFGCGRNSKDRQFIYVNKRPVEYSTLLKCCNEVYKTFNNVQFPAVFLNLELPMSLIDVNVTPDKRVILLHNERAVIDIFKTTLSDYYNRQELALP 364
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhhhhhhhhhhhhh...eeeeeee.....eeeeee.....hhhhh......ee.---------....eeee.hhhhhhhhhh.eeeeeee.....eeeeee.....eeeeeee....eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeee.....hhhhhhhhhhh......eeeeeeeee.hhhh...------------...eeeeeeeee.............eeeee..eee.hhhhhhhhhhhhhh........eeeeee.hhh.ee..........ee.hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------S----------------------------------------------------------------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------DNA_MIS------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3h4l A  42 DVHRITSGQVITDLTTAVKELVDNSIDANANQIEIIFKDYGLESIECSDNGDGIDPSNYEFLALKHYT---------AKVQTLGFRGEALSSLCGIAKLSVITTTSPPKADKLEYDMVGHITSKTTTSRNKGTTVLVSQLFHNLPVRQKEFSKTFKRQFTKCLTVIQGYAIINAAIKFSVWNITPKGKKNLILSTMRNSSMRKNISSVFGAGGMRGLEEVDLVLDLNPFKNRM------------LDYKIRVKGYISQNSFGCGRNSKDRQFIYVNKRPVEYSTLLKCCNEVYKTFNNVQFPAVFLNLELPMSLIDVNVTPDKRVILLHNERAVIDIFKTTLSDYYNRQELALP 395
                                    51        61        71        81        91       101       | -       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271  |      -     | 291       301       311       321       331       341       351       361       371       381       391    
                                                                                             109       119                                                                                                                                                        274          287

Chain B from PDB  Type:PROTEIN  Length:344
 aligned with PMS1_YEAST | P14242 from UniProtKB/Swiss-Prot  Length:873

    Alignment length:357
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       
           PMS1_YEAST     6 QINDIDVHRITSGQVITDLTTAVKELVDNSIDANANQIEIIFKDYGLESIECSDNGDGIDPSNYEFLALKHYTSKIAKFQDVAKVQTLGFRGEALSSLCGIAKLSVITTTSPPKADKLEYDMVGHITSKTTTSRNKGTTVLVSQLFHNLPVRQKEFSKTFKRQFTKCLTVIQGYAIINAAIKFSVWNITPKGKKNLILSTMRNSSMRKNISSVFGAGGMRGLEEVDLVLDLNPFKNRMLGKYTDDPDFLDLDYKIRVKGYISQNSFGCGRNSKDRQFIYVNKRPVEYSTLLKCCNEVYKTFNNVQFPAVFLNLELPMSLIDVNVTPDKRVILLHNERAVIDIFKTTLSDYYNRQELA 362
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...eeeeeee.hhh.eeeeee........hhhhh....hhhhhh...hhhhhh......hhhhhhhhh.eeeeeee....eeeeeee.....eeeeeeee...eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee....eeeeeee.....hhhhhhhhhhhhhhh..eeeeeeeee.hhhh....---------.....eeeeeeeee.............eeeee......hhhhhhhhhhhhhh........eeeeee.hhh.ee----......ee.hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------S----------------------------------------------------------------------T---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------DNA_MIS---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h4l B  37 QINDIDVHRITSGQVITDLTTAVKELVDNSIDANANQIEIIFKDYGLESIECSDNGDGIDPSNYEFLALKHYTSKIAKFQDVAKVQTLGFRGEALSSLCGIAKLSVITTTSPPKADKLEYDMVGHITSKTTTSRNKGTTVLVSQLFHNLPVRQKEFSKTFKRQFTKCLTVIQGYAIINAAIKFSVWNITPKGKKNLILSTMRNSSMRKNISSVFGAGGMRGLEEVDLVLDLNPFKNRML---------LDLDYKIRVKGYISQNSFGCGRNSKDRQFIYVNKRPVEYSTLLKCCNEVYKTFNNVQFPAVFLNLELPMSLID----PDKRVILLHNERAVIDIFKTTLSDYYNRQELA 393
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266        |-       286       296       306       316       326       336       346       356|    | 366       376       386       
                                                                                                                                                                                                                                                                        275       285                                                                     357  362

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 3H4L)

(no "CATH Domain" information available for 3H4L)

(no "Pfam Domain" information available for 3H4L)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PMS1_YEAST | P14242)

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:0032135	DNA insertion or deletion binding	Interacting selectively and non-covalently with double-stranded DNA containing insertions or deletions.
	GO:0032139	dinucleotide insertion or deletion binding	Interacting selectively and non-covalently with double-stranded DNA containing a dinucleotide insertion or deletion.
	GO:0003690	double-stranded DNA binding	Interacting selectively and non-covalently with double-stranded DNA.
	GO:0000404	heteroduplex DNA loop binding	Interacting selectively and non-covalently with DNA containing a loop. A loop occurs when DNA contains a large insertion or deletion that causes a region of unpaired single-stranded DNA to loop out, while the rest of the DNA is in a paired double-stranded configuration.
	GO:0030983	mismatched DNA binding	Interacting selectively and non-covalently with double-stranded DNA containing one or more mismatches.
	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:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
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: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: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.
cellular component
	GO:0032389	MutLalpha complex	A heterodimer involved in the recognition of base-base and small insertion/deletion mismatches. In human the complex consists of two subunits, MLH1 and PMS2.
	GO:0032300	mismatch repair complex	Any complex formed of proteins that act in mismatch repair.
	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.

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	3h4l
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	PMS1_YEAST \| P14242	:	4e4w 4fmn 4fmo

(no "Related Entries Specified in the PDB File" available for 3H4L)

Description

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Ligands, Modified Residues, Ions (2, 4)

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