1IN4 - JenaLib

Title :   THERMOTOGA MARITIMA RUVB HOLLIDAY JUNCTION BRANCH MIGRATION MOTOR

Authors :   C. D. Putnam, J. A. Tainer

Date :   12 May 01 (Deposition) - 08 Aug 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym./Biol. Unit : A

Keywords :   Aaa+-Class Atpase, Winged-Helix Domain, Atp Hydrolysis, Walker A, Walker B, Sensor 1, Sensor 2, Arginine Finger, Holliday Junction, Branch Migration, Dna Translocase, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. D. Putnam, S. B. Clancy, H. Tsuruta, S. Gonzalez, J. G. Wetmur, J. A. Tainer
Structure And Mechanism Of The Ruvb Holliday Junction Branch Migration Motor.
J. Mol. Biol. V. 311 297 2001
PubMed-ID: 11478862 | Reference-DOI: 10.1006/JMBI.2001.4852
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:278 , LEU A:279 , GLY A:313 , ARG A:314 , HOH A:505 , HOH A:590 , HOH A:591 , HEZ A:703 , CO A:705	BINDING SITE FOR RESIDUE ACT A 701
2	AC2	SOFTWARE	ARG A:168 , PHE A:260 , TYR A:297 , HOH A:599	BINDING SITE FOR RESIDUE ACT A 702
3	AC3	SOFTWARE	HOH A:591 , ACT A:701 , HEZ A:703	BINDING SITE FOR RESIDUE CO A 705
4	AC4	SOFTWARE	LEU A:19 , ARG A:20 , PRO A:21 , PHE A:27 , ILE A:28 , GLY A:61 , LEU A:62 , GLY A:63 , LYS A:64 , THR A:65 , THR A:66 , TYR A:180 , PRO A:216 , ARG A:217 , ILE A:220 , HOH A:430 , HOH A:436 , HOH A:531 , HOH A:543 , HOH A:544 , HOH A:551 , HOH A:558	BINDING SITE FOR RESIDUE ADP A 700
5	AC5	SOFTWARE	GLY A:278 , LEU A:279 , ASN A:280 , ALA A:281 , ARG A:312 , HOH A:591 , ACT A:701 , CO A:705	BINDING SITE FOR RESIDUE HEZ A 703
6	AC6	SOFTWARE	GLU A:270 , HOH A:428 , HOH A:585	BINDING SITE FOR RESIDUE HEZ A 704

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:298
 aligned with RUVB_THEMA | Q56313 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:313
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326   
           RUVB_THEMA    17 QFLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQTNIHVTSGPVLVKQGDMAAILTSLERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLVGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGTPRIAIRLTKRVRDMLTVVKADRINTDIVLKTMEVLNIDDEGLDEFDRKILKTIIEIYRGGPVGLNALAASLGVEADTLSEVYEPYLLQAGFLARTPRGRIVTEKAYKHLKYEVP 329
               SCOP domains d1in4a2 A:17-254 Holliday junction helicase RuvB                                                                                                                                                                                              d1in4a1 A:255-329 Holliday junction helicase RuvB                           SCOP domains
               CATH domains 1in4A01 A:17-180 P-loop containing nucleotide triphosphate hydrolases                                                                                               1in4A03 A:181-255  [code=1.10.8.60, no name defined]                       1in4A02 A:256-328 'winged helix' repressor DNA binding domain            - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh..hhhhhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhh...---------------.....eeeeee.hhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhhhhhh..eeee..eeeehhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1in4 A  17 QFLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQTNIHVTSGPVLVKQGDMAAILTSLERGDVLFIDEIHRLNKAVEELLYSAIEDFQI---------------DIQPFTLVGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGTPRIAIRLTKRVRDMLTVVKADRINTDIVLKTMEVLNIDDEGLDEFDRKILKTIIEIYRGGPVGLNALAASLGVEADTLSEVYEPYLLQAGFLARTPRGRIVTEKAYKHLKYEVP 329
                                    26        36        46        56        66        76        86        96       106       116       126    |    -         -|      156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326   
                                                                                                                                            131             147

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 '\|'

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (3, 3)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RUVB_THEMA | Q56313)

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:0009378	four-way junction helicase activity	Catalysis of the unwinding of the DNA helix of DNA containing four-way junctions, including Holliday junctions.
	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: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.
biological process
	GO:0032508	DNA duplex unwinding	The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
	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:0009432	SOS response	An error-prone process for repairing damaged microbial DNA.
	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.

Visualization

Interactive Views

Asymmetric/Biological 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
		ACT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ADP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		HEZ	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:275 - Pro A:276	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1in4
		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
	RUVB_THEMA \| Q56313
		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

Description