4E4W - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF THE C-TERMINAL DOMAIN OF THE SACCHAROMYCES CEREVISIAE MUTL ALPHA (MLH1/PMS1) HETERODIMER

Authors :   E. Gueneau, P. Legrand, J. B. Charbonnier

Date :   13 Mar 12 (Deposition) - 20 Feb 13 (Release) - 19 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Mismatch Repair, Mutl, Endonuclease, Zn-Binding Protein, Dna Damage, Dna Repair, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Gueneau, C. Dherin, P. Legrand, C. Tellier-Lebegue, B. Gilquin, P. Bonnesoeur, F. Londino, C. Quemener, M. H. Le Du, J. A. Marquez, M. Moutiez, M. Gondry, S. Boiteux, J. B. Charbonnier
Structure Of The Mutlalpha C-Terminal Domain Reveals How Mlh1 Contributes To Pms1 Endonuclease Site.
Nat. Struct. Mol. Biol. V. 20 461 2013
PubMed-ID: 23435383 | Reference-DOI: 10.1038/NSMB.2511

Molecule 1 - DNA MISMATCH REPAIR PROTEIN MLH1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 483-769
	Gene	:	MLH1, PMS2, YMR167W, YM8520.16
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE S288C
	Organism Taxid	:	559292
	Strain	:	ATCC 204508 / S288C
	Synonym	:	MUTL PROTEIN HOMOLOG 1

Molecule 2 - DNA MISMATCH REPAIR PROTEIN PMS1
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 635-873
	Gene	:	PMS1, YNL082W, N2317
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE S288C
	Organism Taxid	:	559292
	Strain	:	ATCC 204508 / S288C
	Synonym	:	POSTMEIOTIC SEGREGATION PROTEIN 1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 10)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	5	Ligand/Ion	GLYCEROL
3	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:656 , CYS A:738 , ARG A:741 , ARG A:742 , HOH A:979 , HOH A:992	BINDING SITE FOR RESIDUE GOL A 801
02	AC2	SOFTWARE	ILE A:525 , ARG A:527 , HOH A:940 , ASN B:828 , LYS B:829 , LYS B:830 , HOH B:1030	BINDING SITE FOR RESIDUE GOL A 802
03	AC3	SOFTWARE	ASP A:594 , ILE A:595 , VAL A:596 , ASN A:599 , LEU A:600 , GLU A:603 , HOH A:997	BINDING SITE FOR RESIDUE GOL A 803
04	AC4	SOFTWARE	ASN A:590 , ASP A:593 , HOH A:1013 , ASN B:681	BINDING SITE FOR RESIDUE GOL A 804
05	AC5	SOFTWARE	ILE A:525 , HIS A:526 , ARG A:527 , GLU A:528 , ARG A:747 , HOH B:1027	BINDING SITE FOR RESIDUE GOL A 805
06	AC6	SOFTWARE	ASP A:522 , THR A:576	BINDING SITE FOR RESIDUE EDO A 806
07	AC7	SOFTWARE	ASP A:700 , MET A:701 , HOH A:937 , TYR B:871	BINDING SITE FOR RESIDUE EDO A 807
08	AC8	SOFTWARE	LEU A:517 , LYS A:520 , VAL A:521 , TYR A:571 , ARG A:691 , HOH A:928	BINDING SITE FOR RESIDUE EDO A 808
09	AC9	SOFTWARE	CYS A:769 , HIS B:703 , GLU B:707 , CYS B:817 , ZN B:902	BINDING SITE FOR RESIDUE ZN B 901
10	BC1	SOFTWARE	CYS A:769 , GLU B:707 , CYS B:848 , HIS B:850 , ZN B:901	BINDING SITE FOR RESIDUE ZN B 902

(no "SS Bond" information available for 4E4W)

Asymmetric/Biological Unit

No.	Residues
1	Val B:691	-	Asp B:692

Asymmetric/Biological Unit (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_MLH1_YEAST_011 *	L	607	F	MLH1_YEAST	---	---	A	L	607	F
2	UniProt	VAR_MLH1_YEAST_012 *	D	678	N	MLH1_YEAST	---	---	A	D	678	N
3	UniProt	VAR_MLH1_YEAST_013 *	P	703	L	MLH1_YEAST	---	---	A	P	703	L
4	UniProt	VAR_MLH1_YEAST_014 *	D	761	G	MLH1_YEAST	---	---	A	D	761	G
5	UniProt	VAR_PMS1_YEAST_011 *	K	768	R	PMS1_YEAST	---	---	B	K	768	R
6	UniProt	VAR_PMS1_YEAST_012 *	R	818	K	PMS1_YEAST	---	---	B	R	818	K
	* ID not provided by source

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

(no "PROSITE Motif" information available for 4E4W)

(no "Exon" information available for 4E4W)

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:261
 aligned with MLH1_YEAST | P38920 from UniProtKB/Swiss-Prot  Length:769

    Alignment length:261
                                   518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768 
           MLH1_YEAST   509 VNLTSIKKLREKVDDSIHRELTDIFANLNYVGVVDEERRLAAIQHDLKLFLIDYGSVCYELFYQIGLTDFANFGKINLQSTNVSDDIVLYNLLSEFDELNDDASKEKIISKIWDMSSMLNEYYSIELVNDGLDNDLKSVKLKSLPLLLKGYIPSLVKLPFFIYRLGKEVDWEDEQECLDGILREIALLYIPDMVPKVDTSDASLSEDEKAQFINRKEHISSLLEHVLFPCIKRRFLAPRHILKDVVEIANLPDLYKVFERC 769
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....eeeeee..eeeeeehhhhhhhhhhhhhhhhh...eeee....hhhhh.hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.eeee.....hhh.eeeeeeee..........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.eeeeeehhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------F----------------------------------------------------------------------N------------------------L---------------------------------------------------------G-------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e4w A 509 VNLTSIKKLREKVDDSIHRELTDIFANLNYVGVVDEERRLAAIQHDLKLFLIDYGSVCYELFYQIGLTDFANFGKINLQSTNVSDDIVLYNLLSEFDELNDDASKEKIISKIWDMSSMLNEYYSIELVNDGLDNDLKSVKLKSLPLLLKGYIPSLVKLPFFIYRLGKEVDWEDEQECLDGILREIALLYIPDMVPKVDTSDASLSEDEKAQFINRKEHISSLLEHVLFPCIKRRFLAPRHILKDVVEIANLPDLYKVFERC 769
                                   518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768

Chain B from PDB  Type:PROTEIN  Length:213
 aligned with PMS1_YEAST | P14242 from UniProtKB/Swiss-Prot  Length:873

    Alignment length:225
                                   658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868     
           PMS1_YEAST   649 KDELEDFEQGEKYLTLTVSKNDFKKMEVVGQFNLGFIIVTRKVDNKYDLFIVDQHASDEKYNFETLQAVTVFKSQKLIIPQPVELSVIDELVVLDNLPVFEKNGFKLKIDEEEEFGSRVKLLSLPTSKQTLFDLGDFNELIHLIKEDGGLRRDNIRCSKIRSMFAMRACRSSIMIGKPLNKKTMTRVVHNLSELDKPWNCPHGRPTMRHLMELRDWSSFSKDYEI 873
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee...eeeeeee....eeeeeeehhhhhhhhhhhhhhhhh...eeeeeeeeee...---.hhhhh..hhhhhh......-------..eeeeeee.......hhhhhhhhhhhhhhh--.......hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh............eeeeee.......hhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------R-------------------------------------------------K------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e4w B 649 KDELEDFEQGEKYLTLTVSKNDFKKMEVVGQFNLGFIIVTRKVDNKYDLFIVDQHASDEKYNFETLQAVTVFKSQKLIIPQPVELS---ELVVLDNLPVFEKNGFKLKI-------SRVKLLSLPTSKQTLFDLGDFNELIHLIKED--LRRDNIRCSKIRSMFAMRACRSSIMIGKPLNKKTMTRVVHNLSELDKPWNCPHGRPTMRHLMELRDWSSFSKDYEI 873
                                   658       668       678       688       698       708       718       728     | 738       748        |-      |768       778       788      |798       808       818       828       838       848       858       868     
                                                                                                               734 738                757     765                           795  |                                                                           
                                                                                                                                                                               798

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 4E4W)

(no "CATH Domain" information available for 4E4W)

(no "Pfam Domain" information available for 4E4W)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (MLH1_YEAST | P38920)

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:0000713	meiotic heteroduplex formation	During meiosis, the formation of a stable duplex DNA that contains one strand from each of the two recombining DNA molecules.
	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:0007131	reciprocal meiotic recombination	The cell cycle process in which double strand breaks are formed and repaired through a double Holliday junction intermediate. This results in the equal exchange of genetic material between non-sister chromatids in a pair of homologous chromosomes. These reciprocal recombinant products ensure the proper segregation of homologous chromosomes during meiosis I and create genetic diversity.
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:0097587	MutLgamma complex	A heterodimer involved in the recognition of base-base and small insertion/deletion mismatches. In S. cerevisiae the complex consists of two subunits, Mlh1 and Mlh3.
	GO:0005712	chiasma	A connection formed between chromatids, visible during meiosis, thought to be the point of the interchange involved in crossing-over.
	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:0000795	synaptonemal complex	A proteinaceous scaffold found between homologous chromosomes during meiosis. It consists of 2 lateral elements and a central element, all running parallel to each other. Transverse filaments connect the lateral elements to the central element.

Chain 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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Val B:691 - Asp B:692	[ RasMol ]

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	4e4w
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	MLH1_YEAST \| P38920
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	PMS1_YEAST \| P14242
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	MLH1_YEAST \| P38920	:	4fmn 4fmo
	PMS1_YEAST \| P14242	:	3h4l 4fmn 4fmo

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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SAPs(SNPs)/Variants (6, 6)

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