2PJR | PD0043 - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   HELICASE PRODUCT COMPLEX

Authors :   S. S. Velankar, P. Soultanas, M. S. Dillingham, H. S. Subramanya, D. B. Wigley

Date :   12 Mar 99 (Deposition) - 08 Apr 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym./Biol. Unit : A,B,C,D,F,G,H,I

Keywords :   Helicase Pcra, Hydrolase, Dna, Product Complex, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. S. Velankar, P. Soultanas, M. S. Dillingham, H. S. Subramanya, D. B. Wigley
Crystal Structures Of Complexes Of Pcra Dna Helicase With A Dna Substrate Indicate An Inchworm Mechanism.
Cell(Cambridge, Mass. ) V. 97 75 1999
PubMed-ID: 10199404 | Reference-DOI: 10.1016/S0092-8674(00)80716-3
(for further references see the PDB file header)

*Molecule 1 - DNA (5'-D(TPTPTPTPT)-3')**
	Chains	:	C, D
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - DNA (5'-D(GPC)-3')*
	Chains	:	H
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 3 - DNA (5'-D(APCPTPGPC)-3')**
	Chains	:	I
	Engineered	:	YES
	Synthetic	:	YES

Molecule 4 - PROTEIN (HELICASE PCRA)
	Chains	:	A, F
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 1-548
	Organism Scientific	:	GEOBACILLUS STEAROTHERMOPHILUS
	Organism Taxid	:	1422
	Synonym	:	ATP-DEPENDENT HELICASE PCRA

Molecule 5 - PROTEIN (HELICASE PCRA)
	Chains	:	B, G
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 556-650
	Organism Scientific	:	GEOBACILLUS STEAROTHERMOPHILUS
	Organism Taxid	:	1422
	Synonym	:	ATP-DEPENDENT HELICASE PCRA

		1	2	3	4	5	6	7	8
Asymmetric/Biological Unit	:	A	B	C	D	F	G	H	I

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA F:733 , GLY F:734 , LYS F:737 , GLN F:954 , ARG F:987 , GLY G:1261 , ARG G:1302	BINDING SITE FOR RESIDUE SO4 F 1249
2	AC2	SOFTWARE	ALA A:33 , GLY A:34 , GLN A:254 , ARG A:287 , ARG B:610	BINDING SITE FOR RESIDUE SO4 A 901

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

(no "Cis Peptide Bond" information available for 2PJR)

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

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UVRD_HELICASE_ATP_BIND	PS51198	UvrD-like DNA helicase ATP-binding domain profile.	PCRA_GEOSE	10-289	2	A:10-289 F:710-989
2	UVRD_HELICASE_CTER	PS51217	UvrD-like DNA helicase C-terminal domain profile.	PCRA_GEOSE	290-569	2	A:290-548 F:990-1247

(no "Exon" information available for 2PJR)

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:542
 aligned with PCRA_GEOSE | P56255 from UniProtKB/Swiss-Prot  Length:724

    Alignment length:542
                                    16        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       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546  
          PCRA_GEOSE      7 QLLAHLNKEQQEAVRTTEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLGGAAEDVWISTFHSMCVRILRRDIDRIGINRNFSILDPTDQLSVMKTILKEKNIDPKKFEPRTILGTISAAKNELLPPEQFAKRASTYYEKVVSDVYQEYQQRLLRNHSLDFDDLIMTTIQLFDRVPDVLHYYQYKFQYIHIDEYQDTNRAQYTLVKKLAERFQNICAVGDADQSIYRWRGADIQNILSFERDYPNAKVILLEQNYRSTKRILQAANEVIEHNVNRKPKRIWTENPEGKPILYYEAMNEADEAQFVAGRIREAVERGERRYRDFAVLYRTNAQSRVMEEMLLKANIPYQIVGGLKFYDRKEIKDILAYLRVIANPDDDLSLLRIINVPKRGIGASTIDKLVRYAADHELSLFEALGELEMIGLGAKAAGALAAFRSQLEQWTQLQEYVSVTELVEEVLDKSGYREMLKAERTIEAQSRLENLDEFLSVTKHFENVSDDKSLIAFLTDLALISDLDELD  548
               SCOP domains d2pjra1 A:7-318 DEXX box DNA helicase                                                                                                                                                                                                                                                                                   d2pjr.1 A:319-548,B: DEXX box DNA helicase                                                                                                                                                                                             SCOP domains
               CATH domains ----2pjrA01 A:11-115,A:194-282 P-loop containing nucleotide triphosphate hydrolases                          2pjrA02 A:116-190  [code=1.10.10.160, no name defined]                     ---2pjrA01 A:11-115,A:194-282 P-loop containing nucleotide triphosphate hydrolases          2pjrA03 A:283-385,A:546-548 P-loop containing nucleotide triphosphate hydrolases                       -2pjrA04 A:387-543 PCRA; domain 4                                                                                                                             --2pj CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhh...hhh.eeeee.hhhhhhhhhhhh.....hhhhhheeeehhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh..hhhhhhh.......hhhhhhhhhhhhhhhhh.eee.hhhhhhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh.....eeeeehhhhh.hhhhh.hhhhhhhhhhhh...eeeee.ee...hhhhhhhhhhhhh..........ee.......eeeeee.hhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.......hhhhhhhhhhhhhh...hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---UVRD_HELICASE_ATP_BIND  PDB: A:10-289 UniProt: 10-289                                                                                                                                                                                                                                   UVRD_HELICASE_CTER  PDB: A:290-548 UniProt: 290-569                                                                                                                                                                                                                 PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2pjr A    7 QLLAHLNKEQQEAVRTTEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLGGAAEDVWISTFHSMCVRILRRDIDRIGINRNFSILDPTDQLSVMKTILKEKNIDPKKFEPRTILGTISAAKNELLPPEQFAKRASTYYEKVVSDVYQEYQQRLLRNHSLDFDDLIMTTIQLFDRVPDVLHYYQYKFQYIHIDEYQDTNRAQYTLVKKLAERFQNICAVGDADQSIYRWRGADIQNILSFERDYPNAKVILLEQNYRSTKRILQAANEVIEHNVNRKPKRIWTENPEGKPILYYEAMNEADEAQFVAGRIREAVERGERRYRDFAVLYRTNAQSRVMEEMLLKANIPYQIVGGLKFYDRKEIKDILAYLRVIANPDDDLSLLRIINVPKRGIGASTIDKLVRYAADHELSLFEALGELEMIGLGAKAAGALAAFRSQLEQWTQLQEYVSVTELVEEVLDKSGYREMLKAERTIEAQSRLENLDEFLSVTKHFENVSDDKSLIAFLTDLALISDLDELD  548
                                    16        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       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546

Chain B from PDB  Type:PROTEIN  Length:95
 aligned with PCRA_GEOSE | P56255 from UniProtKB/Swiss-Prot  Length:724

    Alignment length:95
                                   565       575       585       595       605       615       625       635       645     
          PCRA_GEOSE    556 GDAVMLMTLHAAKGLEFPVVFLIGMEEGIFPHNRSLEDDDEMEEERRLAYVGITRAEEELVLTSAQMRTLFGNIQMDPPSRFLNEIPAHLLETAS  650
               SCOP domains d2pjr.1 A:319-548,B: DEXX box DNA helicase                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee........eeeeee..........hhhh.hhhhhhhhhhhhhhhhh.eeeeeeeeee..............hhhhhhhhhh.eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE UVRD_HELICASE_--------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                2pjr B  556 GDAVMLMTLHAAKGLEFPVVFLIGMEEGIFPHNRSLEDDDEMEEERRLAYVGITRAEEELVLTSAQMRTLFGNIQMDPPSRFLNEIPAHLLETAS  650
                                   565       575       585       595       605       615       625       635       645

Chain C from PDB  Type:DNA  Length:5
                                      
                2pjr C   13 TTTTT   17

Chain D from PDB  Type:DNA  Length:5
                                      
                2pjr D   13 TTTTT   17

Chain F from PDB  Type:PROTEIN  Length:544
 aligned with PCRA_GEOSE | P56255 from UniProtKB/Swiss-Prot  Length:724

    Alignment length:544
                                    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       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543    
          PCRA_GEOSE      4 LSEQLLAHLNKEQQEAVRTTEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLGGAAEDVWISTFHSMCVRILRRDIDRIGINRNFSILDPTDQLSVMKTILKEKNIDPKKFEPRTILGTISAAKNELLPPEQFAKRASTYYEKVVSDVYQEYQQRLLRNHSLDFDDLIMTTIQLFDRVPDVLHYYQYKFQYIHIDEYQDTNRAQYTLVKKLAERFQNICAVGDADQSIYRWRGADIQNILSFERDYPNAKVILLEQNYRSTKRILQAANEVIEHNVNRKPKRIWTENPEGKPILYYEAMNEADEAQFVAGRIREAVERGERRYRDFAVLYRTNAQSRVMEEMLLKANIPYQIVGGLKFYDRKEIKDILAYLRVIANPDDDLSLLRIINVPKRGIGASTIDKLVRYAADHELSLFEALGELEMIGLGAKAAGALAAFRSQLEQWTQLQEYVSVTELVEEVLDKSGYREMLKAERTIEAQSRLENLDEFLSVTKHFENVSDDKSLIAFLTDLALISDLDEL  547
               SCOP domains d2pjrf1 F:704-1018 DEXX box DNA helicase                                                                                                                                                                                                                                                                                   d2pjr.2 F:1019-1247,G: DEXX box DNA helicase                                                                                                                                                                                          SCOP domains
               CATH domains -------2pjrF01 F:711-815,F:894-982 P-loop containing nucleotide triphosphate hydrolases                         2pjrF02 F:816-890  [code=1.10.10.160, no name defined]                     ---2pjrF01 F:711-815,F:894-982 P-loop containing nucleotide triphosphate hydrolases         2pjrF03 F:983-1085,F:1246-1247 P-loop containing nucleotide triphosphate hydrolases                    -2pjrF04 F:1087-1243 PCRA; domain 4                                                                                                                           --2p CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhh....eeeee....hhhhhhhhhhhhhh.....hhh.eeeee.hhhhhhhhhhhhh..........eeeehhhhhhhhhhhhhhhhh.....ee.hhhhhhhhhhhhhh.........hhhhhhhhhhhhhh...hhhhhhhh...hhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhh.....eeeeehhhhh........hhhhhhhhhhh...eeeee.ee...hhhhhhhhhhhhh..........ee.......eeeeee.hhhhhhhhhhhhhhhhhh....hhh.eeeee.hhhhhhhhhhhhhhh...eee....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.......hhhhhhhhhhhh.....hhhhhhh..........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhh.....hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------UVRD_HELICASE_ATP_BIND  PDB: F:710-989 UniProt: 10-289                                                                                                                                                                                                                                  UVRD_HELICASE_CTER  PDB: F:990-1247 UniProt: 290-569                                                                                                                                                                                                               PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2pjr F  704 LSEQLLAHLNKEQQEAVRTTEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLGGAAEDVWISTFHSMCVRILRRDIDRIGINRNFSILDPTDQLSVMKTILKEKNIDPKKFEPRTILGTISAAKNELLPPEQFAKRASTYYEKVVSDVYQEYQQRLLRNHSLDFDDLIMTTIQLFDRVPDVLHYYQYKFQYIHIDEYQDTNRAQYTLVKKLAERFQNICAVGDADQSIYRWRGADIQNILSFERDYPNAKVILLEQNYRSTKRILQAANEVIEHNVNRKPKRIWTENPEGKPILYYEAMNEADEAQFVAGRIREAVERGERRYRDFAVLYRTNAQSRVMEEMLLKANIPYQIVGGLKFYDRKEIKDILAYLRVIANPDDDLSLLRIINVPKRGIGASTIDKLVRYAADHELSLFEALGELEMIGLGAKAAGALAAFRSQLEQWTQLQEYVSVTELVEEVLDKSGYREMLKAERTIEAQSRLENLDEFLSVTKHFENVSDDKSLIAFLTDLALISDLDEL 1247
                                   713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923       933       943       953       963       973       983       993      1003      1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243

Chain G from PDB  Type:PROTEIN  Length:95
 aligned with PCRA_GEOSE | P56255 from UniProtKB/Swiss-Prot  Length:724

    Alignment length:95
                                   565       575       585       595       605       615       625       635       645     
          PCRA_GEOSE    556 GDAVMLMTLHAAKGLEFPVVFLIGMEEGIFPHNRSLEDDDEMEEERRLAYVGITRAEEELVLTSAQMRTLFGNIQMDPPSRFLNEIPAHLLETAS  650
               SCOP domains d2pjr.2 F:1019-1247,G: DEXX box DNA helicase                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee........eeeeee..........hhhhh....hhhhhhhhhhhhh.eeeeeeeeee................hhhhh....eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE UVRD_HELICASE_--------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                2pjr G 1248 GDAVMLMTLHAAKGLEFPVVFLIGMEEGIFPHNRSLEDDDEMEEERRLAYVGITRAEEELVLTSAQMRTLFGNIQMDPPSRFLNEIPAHLLETAS 1342
                                  1257      1267      1277      1287      1297      1307      1317      1327      1337

Chain H from PDB  Type:DNA  Length:2
                                   
                2pjr H    1 GC    2

Chain I from PDB  Type:DNA  Length:5
                                      
                2pjr I   30 ACTGC   34

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: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: Tandem AAA-ATPase domain (59)

Protein domain: DEXX box DNA helicase (6)

Bacillus stearothermophilus, PcrA [TaxId: 1422] (5)

1a	d2pjr.1	A:319-548,B:
1b	d2pjr.2	F:1019-1247,G:
1c	d2pjra1	A:7-318
1d	d2pjrf1	F:704-1018

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

[unclassified] (24)

1a	2pjrA01	A:11-115,A:194-282
1b	2pjrF01	F:711-815,F:894-982
1c	2pjrA03	A:283-385,A:546-548
1d	2pjrF03	F:983-1085,F:1246-1247

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: [code=1.10.10.160, no name defined] (9)

[unclassified] (6)

2a	2pjrA02	A:116-190
2b	2pjrF02	F:816-890

Topology: PCRA; domain 4 (12)

Homologous Superfamily: PCRA; domain 4 (12)

[unclassified] (6)

3a	2pjrA04	A:387-543
3b	2pjrF04	F:1087-1243

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,F,G (PCRA_GEOSE | P56255)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004003	ATP-dependent DNA helicase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of the DNA helix.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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: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.
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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	2pjr
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	PCRA_GEOSE \| P56255	:	1pjr 1qhg 1qhh 3pjr 5dma

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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