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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF BACILLUS STEAROTHERMOPHILUS PRFA-HOLLIDAY JUNCTION RESOLVASE

Authors :   J. Li, M. J. Jedrzejas

Date :   12 Dec 05 (Deposition) - 21 Nov 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Flexibility, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. J. Kelly, J. Li, P. Setlow, M. J. Jedrzejas
Structure, Flexibility, And Mechanism Of The Bacillus Stearothermophilus Recu Holliday Junction Resolvase.
Proteins V. 68 961 2007
PubMed-ID: 17557334 | Reference-DOI: 10.1002/PROT.21418

Molecule 1 - RECOMBINATION PROTEIN U (PENICILLIN-BINDING PROTEIN RELATED FACTOR A)
	Chains	:	A, B
	EC Number	:	3.1.22.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET9D
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RECU/PRFA
	Organism Scientific	:	GEOBACILLUS KAUSTOPHILUS
	Organism Taxid	:	235909
	Strain	:	HTA426

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:82 , THR A:84 , ASP A:86 , GLU A:99 , GLN A:118 , HOH A:623	BINDING SITE FOR RESIDUE MG A 701
2	AC2	SOFTWARE	THR B:84 , ASP B:86 , GLU B:99 , GLN B:118 , HOH B:426	BINDING SITE FOR RESIDUE MG B 702
3	AC3	SOFTWARE	TYR B:91 , ASP B:188 , ILE B:190 , ASP B:194	BINDING SITE FOR RESIDUE EDO B 801
4	AC4	SOFTWARE	GLU A:123 , GLN A:124 , HOH A:323 , THR B:107 , ARG B:164 , HOH B:552 , HOH B:562 , HOH B:574	BINDING SITE FOR RESIDUE EDO B 802

(no "SS Bond" information available for 2FCO)

Asymmetric/Biological Unit

No.	Residues
1	Gln A:184	-	Pro A:185
2	Gln B:184	-	Pro B:185

(no "SAP(SNP)/Variant" information available for 2FCO)

(no "PROSITE Motif" information available for 2FCO)

(no "Exon" information available for 2FCO)

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:154
 aligned with RECU_GEOKA | Q5KXY4 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:171
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199 
           RECU_GEOKA    30 GMTLEDDLNATNEYYRERGIAVIHKKPTPVQIVRVDYPKRSAAVITEAYFRQASTTDYNGVYRGKYIDFEAKETKNKTAFPLKNFHAHQIRHMEQVVAHGGICFAILRFSLLNETYLLDASHLIAWWNKQEAGGRKSIPKQEIERHGHSIPLGYQPRIDYISVVDNVYFTR 200
               SCOP domains d2fcoa_ A: automated matches                                                                                                                                                SCOP domains
               CATH domains 2fcoA00 A:30-200  [code=3.40.1                 350.10, no name defined]                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh...eeee.....-----------------..........eeeee..eeeeeeeeee....eee.hhhhhhhhhhhhhhhhh..eeeeeeee....eeeeeehhhhhhhhhhh......eeehhhhhhhhee.........hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fco A  30 GMTLEDDLNATNEYYRERGIAVIHKKPTPV-----------------AYFRQASTTDYNGVYRGKYIDFEAKETKNKTAFPLKNFHAHQIRHMEQVVAHGGICFAILRFSLLNETYLLDASHLIAWWNKQEAGGRKSIPKQEIERHGHSIPLGYQPRIDYISVVDNVYFTR 200
                                    39        49        59         -       |79        89        99       109       119       129       139       149       159       169       179       189       199 
                                                        59                77

Chain B from PDB  Type:PROTEIN  Length:154
 aligned with RECU_GEOKA | Q5KXY4 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:172
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198  
           RECU_GEOKA    29 RGMTLEDDLNATNEYYRERGIAVIHKKPTPVQIVRVDYPKRSAAVITEAYFRQASTTDYNGVYRGKYIDFEAKETKNKTAFPLKNFHAHQIRHMEQVVAHGGICFAILRFSLLNETYLLDASHLIAWWNKQEAGGRKSIPKQEIERHGHSIPLGYQPRIDYISVVDNVYFTR 200
               SCOP domains d2fcob_ B: automated matches                                                                                                                                                 SCOP domains
               CATH domains 2fcoB00 B:29-200  [code=3.40.135                  0.10, no name defined]                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh...eeee......------------------........eeeee..eeeeeeeeee....eee.hhhhhhhhhhhhhhhhh..eeeeeeee.hhheeeeeehhhhhhhhhhhhh....eeehhhhhhhhee.........hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fco B  29 RGMTLEDDLNATNEYYRERGIAVIHKKPTPVQ------------------FRQASTTDYNGVYRGKYIDFEAKETKNKTAFPLKNFHAHQIRHMEQVVAHGGICFAILRFSLLNETYLLDASHLIAWWNKQEAGGRKSIPKQEIERHGHSIPLGYQPRIDYISVVDNVYFTR 200
                                    38        48        58 |       -         -|       88        98       108       118       128       138       148       158       168       178       188       198  
                                                          60                 79

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Restriction endonuclease-like (209)

Superfamily: Restriction endonuclease-like (170)

Family: RecU-like (4)

Protein domain: automated matches (2)

Geobacillus kaustophilus [TaxId: 235909] (1)

1a	d2fcoa_	A:
1b	d2fcob_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Trna Endonuclease; Chain: A, domain 1 (24)

Homologous Superfamily: [code=3.40.1350.10, no name defined] (24)

Geobacillus kaustophilus hta426. Organism_taxid: 235909. Strain: hta426. (1)

1a	2fcoA00	A:30-200
1b	2fcoB00	B:29-200

(no "Pfam Domain" information available for 2FCO)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (RECU_GEOKA | Q5KXY4)

molecular function
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
biological process
	GO:0006310	DNA recombination	Any 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. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
	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:0007059	chromosome segregation	The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gln A:184 - Pro A:185	[ RasMol ]
		Gln B:184 - Pro B:185	[ RasMol ]

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	RECU_GEOKA \| Q5KXY4	:	1y1o

(no "Related Entries Specified in the PDB File" available for 2FCO)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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