1S5J - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   INSIGHT IN DNA REPLICATION: THE CRYSTAL STRUCTURE OF DNA POLYMERASE B1 FROM THE ARCHAEON SULFOLOBUS SOLFATARICUS

Authors :   C. Savino, L. Federici, V. Nastopoulos, K. A. Johnson, F. M. Pisani, M. Rossi, D. Tsernoglou

Date :   21 Jan 04 (Deposition) - 09 Nov 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A

Keywords :   Dna Polymerase, Replication, Disulfide Bonds, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Savino, L. Federici, K. A. Johnson, B. Vallone, V. Nastopoulos, M. Rossi, F. M. Pisani, D. Tsernoglou
Insights Into Dna Replication: The Crystal Structure Of Dna Polymerase B1 From The Archaeon Sulfolobus Solfataricus
Structure V. 12 2001 2004
PubMed-ID: 15530364 | Reference-DOI: 10.1016/J.STR.2004.09.007
(for further references see the PDB file header)

Molecule 1 - DNA POLYMERASE I
	Chains	:	A
	EC Number	:	2.7.7.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PT7-7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	DPO1, POLS, SSO0552
	Organism Scientific	:	SULFOLOBUS SOLFATARICUS
	Organism Taxid	:	2287
	Strain	:	MT 4

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 10)

No.	Name	Count	Type	Full Name
1	MG	1	Ligand/Ion	MAGNESIUM ION
2	SO4	9	Ligand/Ion	SULFATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PRO A:138 , ARG A:142 , LYS A:157 , TYR A:158 , HOH A:1019 , HOH A:1030 , HOH A:1068 , HOH A:1073	BINDING SITE FOR RESIDUE SO4 A 883
02	AC2	SOFTWARE	ARG A:574 , LYS A:579 , LYS A:603 , HOH A:968 , HOH A:1136	BINDING SITE FOR RESIDUE SO4 A 884
03	AC3	SOFTWARE	ILE A:50 , PHE A:52 , LYS A:72 , GLU A:221	BINDING SITE FOR RESIDUE SO4 A 885
04	AC4	SOFTWARE	ALA A:516 , SER A:517 , ASN A:607 , HOH A:968 , HOH A:1132	BINDING SITE FOR RESIDUE SO4 A 886
05	AC5	SOFTWARE	LYS A:87 , ARG A:136 , LYS A:247	BINDING SITE FOR RESIDUE SO4 A 887
06	AC6	SOFTWARE	ARG A:142 , ARG A:145 , HOH A:1010 , HOH A:1057	BINDING SITE FOR RESIDUE SO4 A 888
07	AC7	SOFTWARE	TRP A:41 , GLU A:43 , LYS A:76 , ILE A:77	BINDING SITE FOR RESIDUE SO4 A 889
08	AC8	SOFTWARE	GLU A:276 , PHE A:289 , ASN A:290 , THR A:291 , GLU A:294	BINDING SITE FOR RESIDUE SO4 A 890
09	AC9	SOFTWARE	TYR A:152 , GLU A:475 , LYS A:479	BINDING SITE FOR RESIDUE SO4 A 891
10	BC1	SOFTWARE	ASP A:231 , GLU A:233 , ASP A:413	BINDING SITE FOR RESIDUE MG A 892

Asymmetric/Biological Unit

No.	Residues
1	A:538	-	A:556

(no "Cis Peptide Bond" information available for 1S5J)

(no "SAP(SNP)/Variant" information available for 1S5J)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_POLYMERASE_B	PS00116	DNA polymerase family B signature.	DPOL1_SULSO	653-661	1	A:653-661

(no "Exon" information available for 1S5J)

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:727
 aligned with DPOL1_SULSO | P26811 from UniProtKB/Swiss-Prot  Length:882

    Alignment length:825
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859     
          DPOL1_SULSO    40 EWLEEAQENKIYFLLQVDYDGKKGKAVCKLFDKETQKIYALYDNTGHKPYFLVDLEPDKVGKIPKIVRDPSFDHIETVSKIDPYTWNKFKLTKIVVRDPLAVRRLRNDVPKAYEAHIKYFNNYMYDIGLIPGMPYVVKNGKLESVYLSLDEKDVEEIKKAFADSDEMTRQMAVDWLPIFETEIPKIKRVAIDIEVYTPVKGRIPDSQKAEFPIISIALAGSDGLKKVLVLNRNDVNEGSVKLDGISVERFNTEYELLGRFFDILLEYPIVLTFNGDDFDLPYIYFRALKLGYFPEEIPIDVAGKDEAKYLAGLHIDLYKFFFNKAVRNYAFEGKYNEYNLDAVAKALLGTSKVKVDTLISFLDVEKLIEYNFRDAEITLQLTTFNNDLTMKLIVLFSRISRLGIEELTRTEISTWVKNLYYWEHRKRNWLIPLKEEILAKSSNIRTSALIKGKGYKGAVVIDPPAGIFFNITVLDFASLYPSIIRTWNLSYETVDIQQCKKPYEVKDETGEVLHIVCMDRPGITAVITGLLRDFRVKIYKKKAKNPNNSEEQKLLYDVVQRAMKVFINATYGVFGAETFPLYAPAVAESVTALGRYVITSTVKKAREEGLTVLYGDTDSLFLLNPPKNSLENIIKWVKTTFNLDLEVDKTYKFVAFSGLKKNYFGVYQDGKVDIKGMLVKKRNTPEFVKKVFNEVKELMISINSPNDVKEIKRKIVDVVKGSYEKLKNKGYNLDELAFKVMLSKPLDAYKKNTPQHVKAALQLRPFGVNVLPRDIIYYVKVRSKDGVKPVQLAKVTEIDAEKYLEALRSTFEQILRAFGVSWDEI 864
               SCOP domains d1s5ja1 A:40-449 Exonuclease domain of family B DNA polymerases                                                                                                                                                                                                                                                                                                                                                           d1s5ja2 A:450-864 Family B DNA po              lymerase                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------DNA_pol_B_exo1-1s5jA02 A:72-382                                                                                                                                                                                                                                                                                        --------  ---------------------------------------------------------DNA_pol_B-1s5jA01 A:450-864                                                                                                                                                                                                                                                                                                                                                                                                     Pfam domains
         Sec.struct. author ..........eeeeeeeeee....eeeeeeee....eeeeee.......eeee..hhhhhh.hhhhhh...eeeeeeeeee......eeeeeeeee.hhhhhhhhh.....ee....hhhhhhhhhhh.....eeeee..eeee.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhh......eeeeeeee.................eeeeeeee....eeeeee.........eee..eeeeee.hhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh...hhhhh.ee.......ee...eeeehhhhhhhhhhhhhh........hhhhhhhhhhh..--.........hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhh...--------------........eeeeeeeeeee.hhhhhhhhhh................ee........ee......hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh....eeeee..eeeee..hhhhhhhhhhhhhhhh...eeeeeeeeeeee.----.eeee.......ee....--------..hhhhhhhhhhhh.......hhhhhhhhhhhhhhhh...----------------------------------------------------------------------.....hhhhhhh...hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYM----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s5j A  40 EWLEEAQENKIYFLLQVDYDGKKGKAVCKLFDKETQKIYALYDNTGHKPYFLVDLEPDKVGKIPKIVRDPSFDHIETVSKIDPYTWNKFKLTKIVVRDPLAVRRLRNDVPKAYEAHIKYFNNYMYDIGLIPGMPYVVKNGKLESVYLSLDEKDVEEIKKAFADSDEMTRQMAVDWLPIFETEIPKIKRVAIDIEVYTPVKGRIPDSQKAEFPIISIALAGSDGLKKVLVLNRNDVNEGSVKLDGISVERFNTEYELLGRFFDILLEYPIVLTFNGDDFDLPYIYFRALKLGYFPEEIPIDVAGKDEAKYLAGLHIDLYKFFFNKAVRNYAFEGKYNEYNLDAVAKALLGTS--KVDTLISFLDVEKLIEYNFRDAEITLQLTTFNNDLTMKLIVLFSRISRLGIEELTRTEISTWVKNLYYWEHRKRNWLIPLKEEILAKSSN--------------AVVIDPPAGIFFNITVLDFASLYPSIIRTWNLSYETVDIQQCKKPYEVKDETGEVLHIVCMDRPGITAVITGLLRDFRVKIYKKKAKNPNNSEEQKLLYDVVQRAMKVFINATYGVFGAETFPLYAPRVAESVTALGRYVITSTVKKAREEGLTVLYGDTDSLFLLNPPKNSLENIIKWVKTTFNLDLEVDKTYKFVAFS----NYFGVYQDGKVDIKGMLV--------VKKVFNEVKELMISINSPNDVKEIKRKIVDVVKGSYEKLK----------------------------------------------------------------------IDAEKYLEALRSTFEQILRAFGVSWDEI 864
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389|  |   399       409       419       429       439       449       459       469       479  |      -       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689      |  - |     709        |-       729       739       749       759      |  -         -         -         -         -         -         -       839       849       859     
                                                                                                                                                                                                                                                                                                                                                                                        390  |                                                                                      482            497                                                                                                                                                                                                    696  701              718      727                                    766                                                                    837                           
                                                                                                                                                                                                                                                                                                                                                                                           393

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 "CATH Domain" information available for 1S5J)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DPOL1_SULSO | P26811)

molecular function
	GO:0008408	3'-5' exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003887	DNA-directed DNA polymerase activity	Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
	GO:0004527	exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
	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: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.
	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:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0071897	DNA biosynthetic process	The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ 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 ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1s5j)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites 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
	1s5j
		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
	DPOL1_SULSO \| P26811
		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)
	2.7.7.7
		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
	DPOL1_SULSO \| P26811
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1S5J)

(no "Related Entries Specified in the PDB File" available for 1S5J)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 10)

Sites (10, 10)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (0, 0)

Pfam Domains (2, 2)

Gene Ontology (13, 13)

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