1NHI - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF N-TERMINAL 40KD MUTL (LN40) COMPLEX WITH ADPNP AND ONE POTASSIUM

Authors :   X. Hu, M. Machius, W. Yang

Date :   19 Dec 02 (Deposition) - 10 Jun 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Dna Mismatch Repair, Mutl, Atpase, Rubidium, Replication, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Hu, M. Machius, W. Yang
Monovalent Cation Dependence And Preference Of Ghkl Atpases And Kinases
Febs Lett. V. 544 268 2003
PubMed-ID: 12782329 | Reference-DOI: 10.1016/S0014-5793(03)00519-2

Molecule 1 - DNA MISMATCH REPAIR PROTEIN MUTL
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B PTX418
	Expression System Strain	:	HMS174 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL 40KD ATPASE FRAGMENT (LN40)
	Gene	:	MUTL
	Organism Scientific	:	ESCHERICHIA COLI K12
	Organism Taxid	:	83333
	Strain	:	K-12

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 5)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	K	1	Ligand/Ion	POTASSIUM ION
4	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	ANP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
3	K	-1	Ligand/Ion	POTASSIUM ION
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:33 , ANP A:380 , HOH A:510 , HOH A:622	BINDING SITE FOR RESIDUE MG A 370
2	AC2	SOFTWARE	LEU A:70 , ALA A:71 , ALA A:73 , ALA A:76 , GLY A:96 , ANP A:380 , HOH A:503	BINDING SITE FOR RESIDUE K A 470
3	AC3	SOFTWARE	ARG A:41 , ASP A:43	BINDING SITE FOR RESIDUE EDO A 501
4	AC4	SOFTWARE	LYS A:208 , ARG A:237 , GLY A:238 , TYR A:291	BINDING SITE FOR RESIDUE EDO A 502
5	AC5	SOFTWARE	ILE A:3 , ASN A:33 , ALA A:37 , ASP A:58 , GLY A:62 , ILE A:63 , ALA A:71 , THR A:77 , SER A:78 , LYS A:79 , GLY A:93 , PHE A:94 , ARG A:95 , GLY A:96 , GLU A:97 , ALA A:98 , LEU A:99 , THR A:143 , LYS A:307 , MG A:370 , K A:470 , HOH A:503 , HOH A:511 , HOH A:513 , HOH A:519 , HOH A:582	BINDING SITE FOR RESIDUE ANP A 380

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

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

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

Asymmetric Unit (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.	MUTL_ECO57	93-99	1	A:93-99
1	DNA_MISMATCH_REPAIR_1	PS00058	DNA mismatch repair proteins mutL / hexB / PMS1 signature.	MUTL_ECOLI	93-99	1	A:93-99

Biological Unit 1 (1, 4)

	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.	MUTL_ECO57	93-99	2	A:93-99
1	DNA_MISMATCH_REPAIR_1	PS00058	DNA mismatch repair proteins mutL / hexB / PMS1 signature.	MUTL_ECOLI	93-99	2	A:93-99

(no "Exon" information available for 1NHI)

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 MUTL_ECO57 | Q8XDN4 from UniProtKB/Swiss-Prot  Length:615

    Alignment length:333
                              1                                                                                                                                                                                                                                                                                                                                          
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328   
           MUTL_ECO57     - --MPIQVLPPQLANQIAAGEVVERPASVVKELVENSLDAGATRIDIDIERGGAKLIRIRDNGCGIKKDELALALARHATSKIASLDDLEAIISLGFRGEALASISSVSRLTLTSRTAEQQEAWQAYAEGRDMDVTVKPAAHPVGTTLEVLDLFYNTPARRKFLRTEKTEFNHIDEIIRRIALARFDVTINLSHNGKIVRQYRAVPEGGQKERRLGAICGTAFLEQALAIEWQHGDLTLRGWVADPNHTTPALAEIQYCYVNGRMMRDRLINHAIRQACEDKLGADQQPAFVLYLEIDPHQVDVNVHPAKHEVRFHQSRLVHDFIYQGVLSVLQ 331
               SCOP domains d1nhia2 A:-2-216 DNA mismatch repair protein MutL                                                                                                                                                                         d1nhia1 A:217-331 DNA mismatch repair protein MutL                                                                  SCOP domains
               CATH domains --1nhiA01 A:1-216  [code=3.30.565.10, no name defined]                                                                                                                                                                    1nhiA02 A:217-330  [code=3.30.230.10, no name defined]                                                            - CATH domains
               Pfam domains ----------------------HATPase_c_3-1nhiA01 A:21-142                                                                                              ---------------------------------------------------------------------DNA_mis_repair-1nhiA02 A:212-331                                                                                         Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...eeeeee.hhhh.eeeeee.....hhhhhhhhhh........hhhhhhh........hhhhhhhhh.eeeeeee......eeeeeee....eeeeeee....eeeeeee.....hhhhhh...hhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeee........hhhhhhhhhhhhhhhheeeeeeee..eeeeeeee.hhhh..hhhh.eeeee..eee.hhhhhhhhhhhhhhhh.......eeeeee.hhh.ee..........ee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------------------------------------------------------------------------------------DNA_MIS---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nhi A  -2 SHMPIQVLPPQLANQIAAGEVVERPASVVKELVENSLDAGATRIDIDIERGGAKLIRIRDNGCGIKKDELALALARHATSKIASLDDLEAIISLGFRGEALASISSVSRLTLTSRTAEQQEAWQAYAEGRDMNVTVKPAAHPVGTTLEVLDLFYNTPARRKFLRTEKTEFNHIDEIIRRIALARFDVTINLSHNGKIVRQYRAVPEGGQKERRLGAICGTAFLEQALAIEWQHGDLTLRGWVADPNHTTPALAEIQYCYVNGRMMRDRLINHAIRQACEDKLGADQQPAFVLYLEIDPHQVDVNVHPAKHEVRFHQSRLVHDFIYQGVLSVLQ 331
                             ||      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328   
                             ||                                                                                                                                                                                                                                                                                                                                          
                            -1|                                                                                                                                                                                                                                                                                                                                          
                              1

Chain A from PDB  Type:PROTEIN  Length:333
 aligned with MUTL_ECOLI | P23367 from UniProtKB/Swiss-Prot  Length:615

    Alignment length:333
                              1                                                                                                                                                                                                                                                                                                                                          
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328   
           MUTL_ECOLI     - --MPIQVLPPQLANQIAAGEVVERPASVVKELVENSLDAGATRIDIDIERGGAKLIRIRDNGCGIKKDELALALARHATSKIASLDDLEAIISLGFRGEALASISSVSRLTLTSRTAEQQEAWQAYAEGRDMNVTVKPAAHPVGTTLEVLDLFYNTPARRKFLRTEKTEFNHIDEIIRRIALARFDVTINLSHNGKIVRQYRAVPEGGQKERRLGAICGTAFLEQALAIEWQHGDLTLRGWVADPNHTTPALAEIQYCYVNGRMMRDRLINHAIRQACEDKLGADQQPAFVLYLEIDPHQVDVNVHPAKHEVRFHQSRLVHDFIYQGVLSVLQ 331
               SCOP domains d1nhia2 A:-2-216 DNA mismatch repair protein MutL                                                                                                                                                                         d1nhia1 A:217-331 DNA mismatch repair protein MutL                                                                  SCOP domains
               CATH domains --1nhiA01 A:1-216  [code=3.30.565.10, no name defined]                                                                                                                                                                    1nhiA02 A:217-330  [code=3.30.230.10, no name defined]                                                            - CATH domains
               Pfam domains ----------------------HATPase_c_3-1nhiA01 A:21-142                                                                                              ---------------------------------------------------------------------DNA_mis_repair-1nhiA02 A:212-331                                                                                         Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...eeeeee.hhhh.eeeeee.....hhhhhhhhhh........hhhhhhh........hhhhhhhhh.eeeeeee......eeeeeee....eeeeeee....eeeeeee.....hhhhhh...hhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeee........hhhhhhhhhhhhhhhheeeeeeee..eeeeeeee.hhhh..hhhh.eeeee..eee.hhhhhhhhhhhhhhhh.......eeeeee.hhh.ee..........ee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------DNA_MIS---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nhi A  -2 SHMPIQVLPPQLANQIAAGEVVERPASVVKELVENSLDAGATRIDIDIERGGAKLIRIRDNGCGIKKDELALALARHATSKIASLDDLEAIISLGFRGEALASISSVSRLTLTSRTAEQQEAWQAYAEGRDMNVTVKPAAHPVGTTLEVLDLFYNTPARRKFLRTEKTEFNHIDEIIRRIALARFDVTINLSHNGKIVRQYRAVPEGGQKERRLGAICGTAFLEQALAIEWQHGDLTLRGWVADPNHTTPALAEIQYCYVNGRMMRDRLINHAIRQACEDKLGADQQPAFVLYLEIDPHQVDVNVHPAKHEVRFHQSRLVHDFIYQGVLSVLQ 331
                             ||      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328   
                            -1|                                                                                                                                                                                                                                                                                                                                          
                              1

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

Clans(

)

Families(

)

Organisms( (-)

)

Clan: His_Kinase_A (147)

Family: HATPase_c_3 (11)

Escherichia coli (strain K12) (3)

HATPase_c_3-1nhiA01

A:21-142

Clan: S5 (103)

Family: DNA_mis_repair (3)

Escherichia coli (strain K12) (3)

DNA_mis_repair-1nhiA02

A:212-331

Asymmetric Unit(hide GO term definitions)

Chain A (MUTL_ECO57 | Q8XDN4)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0030983	mismatched DNA binding	Interacting selectively and non-covalently with double-stranded DNA containing one or more mismatches.
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.

Chain A (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.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1nhi)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	1nhi
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	MUTL_ECO57 \| Q8XDN4
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	MUTL_ECOLI \| P23367
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	MUTL_ECO57 \| Q8XDN4
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UniProtKB/Swiss-Prot
	MUTL_ECO57 \| Q8XDN4	:	1nhh 1nhj
	MUTL_ECOLI \| P23367	:	1b62 1b63 1bkn 1nhh 1nhj 1x9z 5akb 5akc 5akd

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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SCOP Domains (2, 2)

CATH Domains (2, 2)

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Gene Ontology (13, 18)

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