1X9Z - JenaLib

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Biological Unit 5 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE MUTL C-TERMINAL DOMAIN

Authors :   A. Guarne, S. Ramon-Maiques, E. M. Wolff, R. Ghirlando, X. Hu, J. H. Mill

Date :   24 Aug 04 (Deposition) - 26 Oct 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A (2x),B (2x)
Biol. Unit 3: A,B  (2x)
Biol. Unit 4: A  (2x)
Biol. Unit 5: B  (2x)

Keywords :   Alpha-Beta Fold, Dimer, Replication, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Guarne, S. Ramon-Maiques, E. M. Wolff, R. Ghirlando, X. Hu, J. H. Miller, W. Yang
Structure Of The Mutl C-Terminal Domain: A Model Of Intact Mutl And Its Roles In Mismatch Repair
Embo J. V. 23 4134 2004
PubMed-ID: 15470502 | Reference-DOI: 10.1038/SJ.EMBOJ.7600412

Molecule 1 - DNA MISMATCH REPAIR PROTEIN MUTL
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	B834DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL DOMAIN
	Gene	:	MUTL
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:	A (2x)	B (2x)
Biological Unit 3 (2x)	:	A	B
Biological Unit 4 (2x)	:	A
Biological Unit 5 (2x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 11)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	IPA	2	Ligand/Ion	ISOPROPYL ALCOHOL
4	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
5	NA	1	Ligand/Ion	SODIUM ION

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	IPA	2	Ligand/Ion	ISOPROPYL ALCOHOL
4	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
5	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (3, 8)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	IPA	2	Ligand/Ion	ISOPROPYL ALCOHOL
4	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
5	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 3 (3, 16)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	4	Ligand/Ion	GLYCEROL
3	IPA	4	Ligand/Ion	ISOPROPYL ALCOHOL
4	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
5	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 4 (3, 8)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	IPA	2	Ligand/Ion	ISOPROPYL ALCOHOL
4	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
5	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 5 (3, 8)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	IPA	2	Ligand/Ion	ISOPROPYL ALCOHOL
4	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
5	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:32 , HOH A:54 , MSE A:574 , ALA B:575	BINDING SITE FOR RESIDUE CL A 421
2	AC2	SOFTWARE	MSE A:574 , ALA A:575 , HOH B:59 , MSE B:574	BINDING SITE FOR RESIDUE CL A 422
3	AC3	SOFTWARE	HOH A:107 , HOH A:239 , GLU A:568 , GLU B:496	BINDING SITE FOR RESIDUE NA A 423
4	AC4	SOFTWARE	HOH A:267 , ASP A:445 , CYS A:446 , SER A:459 , LYS A:613	BINDING SITE FOR RESIDUE GOL A 401
5	AC5	SOFTWARE	HOH B:251 , VAL B:479 , CYS B:480 , GLU B:509	BINDING SITE FOR RESIDUE GOL B 402
6	AC6	SOFTWARE	HOH A:230 , HOH A:304 , PRO A:461 , GLU A:464 , ARG A:468 , SER A:567 , HIS A:569	BINDING SITE FOR RESIDUE IPA A 411
7	AC7	SOFTWARE	GLN B:504 , ASP B:513 , ARG B:524	BINDING SITE FOR RESIDUE IPA B 412

(no "SS Bond" information available for 1X9Z)

(no "Cis Peptide Bond" information available for 1X9Z)

(no "SAP(SNP)/Variant" information available for 1X9Z)

(no "PROSITE Motif" information available for 1X9Z)

(no "Exon" information available for 1X9Z)

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:182
 aligned with MUTL_ECOLI | P23367 from UniProtKB/Swiss-Prot  Length:615

    Alignment length:182
                                   442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612  
           MUTL_ECOLI   433 QSFGRVLTIVHSDCALLERDGNISLLSLPVAERWLRQAQLTPGEAPVCAQPLLIPLRLKVSAEEKSALEKAQSALAELGIDFQSDAQHVTIRAVPLPLRQQNLQILIPELIGYLAKQSVFEPGNIAQWIARNLMSEHAQWSMAQAITLLADVERLCPQLVKTPPGGLLQSVDLHPAIKALKD 614
               SCOP domains d1x9za_ A: DNA mismatch repair protein MutL                                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...eeeeee..eeeeeehhhhhhhhhhhhhh.......eeeeeeeeeee.hhhhhhhhhhhhhhhhhh..eeee...eeeeeeee.hhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh.....eee..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x9z A 433 QSFGRVLTIVHSDCALLERDGNISLLSLPVAERWLRQAQLTPGEAPVCAQPLLIPLRLKVSAEEKSALEKAQSALAELGIDFQSDAQHVTIRAVPLPLRQQNLQILIPELIGYLAKQSVFEPGNIAQWIARNLmSEHAQWSmAQAITLLADVERLCPQLVKTPPGGLLQSVDLHPAIKALKD 614
                                   442       452       462       472       482       492       502       512       522       532       542       552       562   |   572 |     582       592       602       612  
                                                                                                                                                               566-MSE 574-MSE

Chain B from PDB  Type:PROTEIN  Length:182
 aligned with MUTL_ECOLI | P23367 from UniProtKB/Swiss-Prot  Length:615

    Alignment length:182
                                   441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611  
           MUTL_ECOLI   432 SQSFGRVLTIVHSDCALLERDGNISLLSLPVAERWLRQAQLTPGEAPVCAQPLLIPLRLKVSAEEKSALEKAQSALAELGIDFQSDAQHVTIRAVPLPLRQQNLQILIPELIGYLAKQSVFEPGNIAQWIARNLMSEHAQWSMAQAITLLADVERLCPQLVKTPPGGLLQSVDLHPAIKALK 613
               SCOP domains d1x9zb_ B: DNA mismatch repair protein MutL                                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --MutL_C-1x9zB01 B:434-572                                                                                                                   ----------------------------------------- Pfam domains (1)
           Pfam domains (2) --MutL_C-1x9zB02 B:434-572                                                                                                                   ----------------------------------------- Pfam domains (2)
         Sec.struct. author .....eeeeee...eeeeee..eeeeeehhhhhhhhhhhhhh........eeeeeeeeee.hhhhhhhhhhhhhhhhhh..eeee...eeeeeeehhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.....eee..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x9z B 432 SQSFGRVLTIVHSDCALLERDGNISLLSLPVAERWLRQAQLTPGEAPVCAQPLLIPLRLKVSAEEKSALEKAQSALAELGIDFQSDAQHVTIRAVPLPLRQQNLQILIPELIGYLAKQSVFEPGNIAQWIARNLmSEHAQWSmAQAITLLADVERLCPQLVKTPPGGLLQSVDLHPAIKALK 613
                                   441       451       461       471       481       491       501       511       521       531       541       551       561    |  571  |    581       591       601       611  
                                                                                                                                                                566-MSE 574-MSE

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: DNA mismatch repair protein MutL (1)

Superfamily: DNA mismatch repair protein MutL (1)

Family: DNA mismatch repair protein MutL (1)

Protein domain: DNA mismatch repair protein MutL (1)

Escherichia coli [TaxId: 562] (1)

1a	d1x9za_	A:
1b	d1x9zb_	B:

(no "CATH Domain" information available for 1X9Z)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: MutL_C] (4)

Family: MutL_C (4)

Escherichia coli (strain K12) (1)

1a	MutL_C-1x9zB01	B:434-572
1b	MutL_C-1x9zB02	B:434-572

Asymmetric Unit(hide GO term definitions)

Chain A,B (MUTL_ECOLI | P23367)

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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0030983	mismatched DNA binding	Interacting selectively and non-covalently with double-stranded DNA containing one or more mismatches.
	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: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: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:0000018	regulation of DNA recombination	Any process that modulates the frequency, rate or extent of DNA recombination, a DNA metabolic process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents.
cellular component
	GO:0032300	mismatch repair complex	Any complex formed of proteins that act in mismatch repair.

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	Cis Peptide Bonds
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	1x9z
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	MUTL_ECOLI \| P23367	:	1b62 1b63 1bkn 1nhh 1nhi 1nhj 5akb 5akc 5akd

1bkn	THE MUTL N-TERMINAL DOMAIN WITHOUT ADPNP
1nhi	CRYSTAL STRUCTURE OF THE MUTL N-TERMINAL DOMAIN WITH ADPNP AND K+ ION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 11)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Gene Ontology (13, 13)

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