4O4K - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   DNA DOUBLE-STRAND BREAK REPAIR PATHWAY CHOICE IS DIRECTED BY DISTINCT MRE11 NUCLEASE ACTIVITIES

Authors :   A. Shibata, D. Moiani, A. S. Arvai, J. Perry, S. M. Harding, M. Genois, R. S. Rossum-Fikkert, A. Kertokalio, F. Romoli, A. Ismail, E. Ismalaj, E. Petricci, M. J. Neale, R. G. Bristow, J. Masson, C. Wyman, P. A. Jeggo J. A. Tainer

Date :   18 Dec 13 (Deposition) - 08 Jan 14 (Release) - 05 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Dna Repair Dna Double-Strand Break Repair Thermophilic Mre11, Dna Repair Dna Double-Strand Break Repair, Dna Binding Protein-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Shibata, D. Moiani, A. S. Arvai, J. Perry, S. M. Harding, M. M. Genois R. Maity, S. Van Rossum-Fikkert, A. Kertokalio, F. Romoli, A. Ismail E. Ismalaj, E. Petricci, M. J. Neale, R. G. Bristow, J. Y. Masson, C. Wyman, P. A. Jeggo, J. A. Tainer
Dna Double-Strand Break Repair Pathway Choice Is Directed B Distinct Mre11 Nuclease Activities.
Mol. Cell V. 53 7 2014
PubMed-ID: 24316220 | Reference-DOI: 10.1016/J.MOLCEL.2013.11.003

Molecule 1 - EXONUCLEASE, PUTATIVE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	TM_1635
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	243274
	Strain	:	ATCC 43589 / MSB8 / DSM 3109 / JCM 10099

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	2PK	2	Ligand/Ion	2-AMINO-5-(4-HYDROXYBENZYL)-4H-1LAMBDA~4~,3-THIAZOL-4-ONE
2	MN	4	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	2PK	1	Ligand/Ion	2-AMINO-5-(4-HYDROXYBENZYL)-4H-1LAMBDA~4~,3-THIAZOL-4-ONE
2	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	2PK	1	Ligand/Ion	2-AMINO-5-(4-HYDROXYBENZYL)-4H-1LAMBDA~4~,3-THIAZOL-4-ONE
2	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	2PK	2	Ligand/Ion	2-AMINO-5-(4-HYDROXYBENZYL)-4H-1LAMBDA~4~,3-THIAZOL-4-ONE
2	MN	-1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:58 , HIS A:180 , HIS A:216	BINDING SITE FOR RESIDUE MN A 401
2	AC2	SOFTWARE	ASP A:14 , HIS A:16 , ASP A:58 , HIS A:216 , HIS A:218	BINDING SITE FOR RESIDUE MN A 402
3	AC3	SOFTWARE	ASP A:58 , LEU A:59 , LEU A:60 , ARG A:63 , VAL A:89 , ASN A:93 , HIS A:94 , LEU A:99	BINDING SITE FOR RESIDUE 2PK A 403
4	AC4	SOFTWARE	ASP B:58 , HIS B:180 , HIS B:216	BINDING SITE FOR RESIDUE MN B 401
5	AC5	SOFTWARE	ASP B:14 , HIS B:16 , ASP B:58 , HIS B:216 , HIS B:218	BINDING SITE FOR RESIDUE MN B 402
6	AC6	SOFTWARE	GLY B:57 , ASP B:58 , LEU B:59 , LEU B:60 , SER B:62 , ARG B:63 , VAL B:89 , PRO B:91 , GLY B:92 , ASN B:93 , HIS B:94	BINDING SITE FOR RESIDUE 2PK B 403

(no "SS Bond" information available for 4O4K)

Asymmetric Unit

No.	Residues
1	Ala A:187	-	Gly A:188
2	Gln A:226	-	Pro A:227
3	Asp B:141	-	Glu B:142
4	Glu B:142	-	Ser B:143
5	Ala B:145	-	Leu B:146
6	Arg B:147	-	Lys B:148
7	Tyr B:189	-	Ala B:190
8	Ile B:192	-	Glu B:193
9	Gln B:194	-	Gly B:195
10	Gln B:226	-	Pro B:227

(no "SAP(SNP)/Variant" information available for 4O4K)

(no "PROSITE Motif" information available for 4O4K)

(no "Exon" information available for 4O4K)

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:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeee......ee......eehhhhhhhhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhhhhhh.eee.......hhhhhhhhhhhhhh..eee......eeee.....eeeeeee...........hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.ee...............eehhhhh.....eeeee.....eeee....eee.......hhhhh....eeeeeeee.....eeeeee.....eeeeeeee.hhhhhhhhhhhhhhh..eeeeeeee......hhhhhh..eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o4k A  -6 IHHHHHHVINLKELKILHTSDWHLGVTSWTSSRPVDRREELKKALDKVVEEAEKREVDLILLTGDLLHSRNNPSVVALHDLLDYLKRMMRTAPVVVLPGNHDWKGLKLFGNFVTSISSDITFVMSFEPVDVEAKRGQKVRILPFPYPDESEALRKNEGDFRFFLESRLNKLYEEALKKEDFAIFMGHFTVEGLAGYAGIEQGREIIINRALIPSVVDYAALGHIHSFREIQKQPLTIYPGSLIRIDFGEEADEKGAVFVELKRGEPPRYERIDASPLPLKTLYYKKIDTSALKSIRDFCRNFPGYVRVVYEEDSGILPDLMGEIDNLVKIE 324
                                     3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323

Chain B from PDB  Type:PROTEIN  Length:321
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee......ee......eehhhhhhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhhhhh.eee.......hhhhhhhhhhhhhh..eee......eeee.....eeeeeee...........hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.ee...............eehhhhh.....eeeee.....eeee....eee.......hhhhh....eeeeeeee.....eeeeee.....eeeeee...hhhhhhhhhhhhhhh..eeeeee........hhhhhh..eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o4k B   4 LKELKILHTSDWHLGVTSWTSSRPVDRREELKKALDKVVEEAEKREVDLILLTGDLLHSRNNPSVVALHDLLDYLKRMMRTAPVVVLPGNHDWKGLKLFGNFVTSISSDITFVMSFEPVDVEAKRGQKVRILPFPYPDESEALRKNEGDFRFFLESRLNKLYEEALKKEDFAIFMGHFTVEGLAGYAGIEQGREIIINRALIPSVVDYAALGHIHSFREIQKQPLTIYPGSLIRIDFGEEADEKGAVFVELKRGEPPRYERIDASPLPLKTLYYKKIDTSALKSIRDFCRNFPGYVRVVYEEDSGILPDLMGEIDNLVKIE 324
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323

Legend:		→ Mismatch	(orange background)
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	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 4O4K)

(no "CATH Domain" information available for 4O4K)

(no "Pfam Domain" information available for 4O4K)

Asymmetric Unit(hide GO term definitions)

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		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:187 - Gly A:188	[ RasMol ]
		Ala B:145 - Leu B:146	[ RasMol ]
		Arg B:147 - Lys B:148	[ RasMol ]
		Asp B:141 - Glu B:142	[ RasMol ]
		Gln A:226 - Pro A:227	[ RasMol ]
		Gln B:194 - Gly B:195	[ RasMol ]
		Gln B:226 - Pro B:227	[ RasMol ]
		Glu B:142 - Ser B:143	[ RasMol ]
		Ile B:192 - Glu B:193	[ RasMol ]
		Tyr B:189 - Ala B:190	[ RasMol ]

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		Biological Unit 2	[ Jena3D ]
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Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (10, 10)

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