3P4X - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   HELICASE DOMAIN OF REVERSE GYRASE FROM THERMOTOGA MARITIMA

Authors :   M. G. Rudolph, D. Klostermeier

Date :   07 Oct 10 (Deposition) - 15 Jun 11 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.41

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

Keywords :   Topoisomerase, Dna Supercoiling, Archaea, Helicase, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Del Toro Duany, D. Klostermeier, M. G. Rudolph
The Conformational Flexibility Of The Helicase-Like Domain From Thermotoga Maritima Reverse Gyrase Is Restricted By Th Topoisomerase Domain.
Biochemistry V. 50 5816 2011
PubMed-ID: 21627332 | Reference-DOI: 10.1021/BI200236A

Molecule 1 - REVERSE GYRASE HELICASE-LIKE DOMAIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	CL	1	Ligand/Ion	CHLORIDE ION
3	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ADP	-1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:32 , HOH A:33 , HOH A:34 , HOH A:35 , THR A:107 , ADP A:800	BINDING SITE FOR RESIDUE MG A 799
2	AC2	SOFTWARE	HOH A:34 , HOH A:35 , PHE A:71 , PHE A:75 , LYS A:77 , ASP A:78 , THR A:80 , GLN A:83 , THR A:102 , GLY A:103 , VAL A:104 , GLY A:105 , LYS A:106 , THR A:107 , THR A:108 , MG A:799	BINDING SITE FOR RESIDUE ADP A 800
3	AC3	SOFTWARE	GLY B:105 , THR B:108 , ARG B:140	BINDING SITE FOR RESIDUE CL B 1

(no "SS Bond" information available for 3P4X)

Asymmetric Unit

No.	Residues
1	Gly A:389	-	Pro A:460
2	Gly B:389	-	Pro B:460

(no "SAP(SNP)/Variant" information available for 3P4X)

(no "PROSITE Motif" information available for 3P4X)

(no "Exon" information available for 3P4X)

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:399
 aligned with RGYR_THEMA | O51934 from UniProtKB/Swiss-Prot  Length:1104

    Alignment length:477
                                    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       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       
           RGYR_THEMA    59 EFWNEYEDFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTVGRLVSVARNITHVRISSRSKEKLVELLEIFRDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEFEKNFEDFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSMRFSLELDKAPRFVLARVLKEMGLIKAQENPDVEELRKIAKEHLTQKEFVEKVKEMFRGVVVKDEDLELIIPDVYTYIQASGRSSRILNGVLVKGVSVIFEEDEEIFESLKTRLLLIAEEEIIEEAEANWKELVHEVEESRRRSERE 535
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhh.....eee.....hhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhh.....eeee.hhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhh.............eeeeee......hhhhhhhhhhh.............eeeeee...hhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhh...eee...hhhhhhhhhhhh...eeeee...--------.......eeeee.....----------------------------------------------------------------------.hhhhhhhhhhh...ee..ee..eeeeee..hhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p4x A  59 EFWNEYEDFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTVGRLVSVARNITHVRISSRSKEKLVELLEIFRDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEFEKNFEDFKVGKINILIGVQAY--------DLPERIKYVIFWGTPSG----------------------------------------------------------------------PDVYTYIQASGRSSRILNGVLVKGVSVIFEEDEEIFESLKTRLLLIAEEEIIEEAEANWKELVHEVEESRRRSERE 535
                                    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       338       348       358     |   -    |  378       388|        -         -         -         -         -         -         - |     468       478       488       498       508       518       528       
                                                                                                                                                                                                                                                                                                                                           364      373             389                                                                    460

Chain B from PDB  Type:PROTEIN  Length:410
 aligned with RGYR_THEMA | O51934 from UniProtKB/Swiss-Prot  Length:1104

    Alignment length:480
                                    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       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538
           RGYR_THEMA    59 EFWNEYEDFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTVGRLVSVARNITHVRISSRSKEKLVELLEIFRDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEFEKNFEDFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSMRFSLELDKAPRFVLARVLKEMGLIKAQENPDVEELRKIAKEHLTQKEFVEKVKEMFRGVVVKDEDLELIIPDVYTYIQASGRSSRILNGVLVKGVSVIFEEDEEIFESLKTRLLLIAEEEIIEEAEANWKELVHEVEESRRRSERELTD 538
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---------------------DEAD-3p4xB01 B:80-267                                                                                                                                                                       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------DEAD-3p4xB02 B:80-267                                                                                                                                                                       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...ee.......hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.............eeee.........hhhhhhhhhhh..hhhhh.....eeeeee...hhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhh...eee...hhhhhhhhhhhh...eeeee....hhhhhh........eeeee.....----------------------------------------------------------------------.hhhhhhhhhhhhh.ee..ee..eeeeee..hhhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p4x B  59 EFWNEYEDFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTVGRLVSVARNITHVRISSRSKEKLVELLEIFRDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEFEKNFEDFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSG----------------------------------------------------------------------PDVYTYIQASGRSSRILNGVLVKGVSVIFEEDEEIFESLKTRLLLIAEEEIIEEAEANWKELVHEVEESRRRSERELTD 538
                                    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       338       348       358       368       378       388|        -         -         -         -         -         -         - |     468       478       488       498       508       518       528       538
                                                                                                                                                                                                                                                                                                                                                                    389                                                                    460

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 3P4X)

(no "CATH Domain" information available for 3P4X)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: DEAD (41)

Thermotoga maritima (2)

1a	DEAD-3p4xB01	B:80-267
1b	DEAD-3p4xB02	B:80-267

Asymmetric Unit(hide GO term definitions)

Chain A,B (RGYR_THEMA | O51934)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003916	DNA topoisomerase activity	Catalysis of the transient cleavage and passage of individual DNA strands or double helices through one another, resulting a topological transformation in double-stranded DNA.
	GO:0003917	DNA topoisomerase type I activity	Catalysis of a DNA topological transformation by transiently cleaving one DNA strand at a time to allow passage of another strand; changes the linking number by +1 per catalytic cycle.
	GO:0003918	DNA topoisomerase type II (ATP-hydrolyzing) activity	Catalysis of a DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined; product release is coupled to ATP binding and hydrolysis; changes the linking number in multiples of 2.
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	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:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	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:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006265	DNA topological change	The process in which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number.
	GO:0006268	DNA unwinding involved in DNA replication	The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating unpaired template strands for DNA replication.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ADP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:389 - Pro A:460	[ RasMol ]
		Gly B:389 - Pro B:460	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3p4x
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	RGYR_THEMA \| O51934
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	RGYR_THEMA \| O51934
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	RGYR_THEMA \| O51934	:	3p4y 4ddt 4ddu 4ddv 4ddw 4ddx

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (15, 15)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File