O41026 (O41026_PBCV1) Unreviewed, UniProtKB/TrEMBL

Names and origin

Protein names

Submitted name:
ATP-dependent DNA ligase EMBL AAC96909.1

Gene names

Name:

A544R EMBL AAC96909.1

Organism

Paramecium bursaria Chlorella virus 1 (PBCV-1) EMBL AAC96909.1

Taxonomic identifier

10506 [NCBI]

Taxonomic lineage

Viruses › dsDNA viruses, no RNA stage › Phycodnaviridae › Chlorovirus

Virus host

Chlorella [TaxID: 114049]

Protein attributes

Sequence length	298 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

Ontologies

Keywords
Ligand	Nucleotide-binding PDB 1FVI PDB 1P8L PDB 2Q2T
Molecular function	Ligase EMBL AAC96909.1
Technical term	3D-structure PDB 1FVI PDB 1P8L PDB 2Q2T PDB 2Q2U Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	DNA ligation involved in DNA repair Inferred from electronic annotation. Source: InterPro DNA recombination Inferred from electronic annotation. Source: InterPro
Molecular function	ATP binding Inferred from electronic annotation. Source: InterPro DNA ligase (ATP) activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Regions
	Nucleotide binding	25 – 28	4	AMP PDB 1FVI PDB 1P8L PDB 2Q2T
	Nucleotide binding	186 – 188	3	AMP PDB 1FVI PDB 1P8L PDB 2Q2T
Sites
	Binding site	32	1	AMP PDB 2Q2T
	Binding site	67	1	AMP PDB 1P8L PDB 2Q2T
	Binding site	98	1	AMP PDB 1FVI PDB 1P8L PDB 2Q2T

Sequences

	Sequence		Length	Mass (Da)
	O41026 [UniParc]. Last modified January 1, 1998. Version 1. Checksum: 01E5A8094FF558F8	FASTA	298	34,250
	10 20 30 40 50 60 MAITKPLLAA TLENIEDVQF PCLATPKIDG IRSVKQTQML SRTFKPIRNS VMNRLLTELL 70 80 90 100 110 120 PEGSDGEISI EGATFQDTTS AVMTGHKMYN AKFSYYWFDY VTDDPLKKYI DRVEDMKNYI 130 140 150 160 170 180 TVHPHILEHA QVKIIPLIPV EINNITELLQ YERDVLSKGF EGVMIRKPDG KYKFGRSTLK 190 200 210 220 230 240 EGILLKMKQF KDAEATIISM TALFKNTNTK TKDNFGYSKR STHKSGKVEE DVMGSIEVDY 250 260 270 280 290 DGVVFSIGTG FDADQRRDFW QNKESYIGKM VKFKYFEMGS KDCPRFPVFI GIRHEEDR

References

[1]	"Analysis of 45 kb of DNA located at the left end of the chlorella virus PBCV-1 genome." Lu Z., Li Y., Zhang Y., Kutish G.F., Rock D.L., van Etten J.L. Virology 206:339-352(1995) [PubMed: 7831789] [Abstract] Cited for: NUCLEOTIDE SEQUENCE.
[2]	"Analysis of 43 kb of the Chlorella virus PBCV-1 330-kb genome: map positions 45 to 88." Li Y., Lu Z., Burbank D.E., Kutish G.F., Rock D.L., Etten J.L. Virology 212:134-150(1995) [PubMed: 7676624] [Abstract] Cited for: NUCLEOTIDE SEQUENCE.
[3]	"Analysis of 94 kb of the chlorella virus PBCV-1 330-kb genome: map positions 88 to 182." Lu Z., Li Y., Que Q., Kutish G.F., Rock D.L., van Etten J.L. Virology 216:102-123(1996) [PubMed: 8614977] [Abstract] Cited for: NUCLEOTIDE SEQUENCE.
[4]	"Analysis of 76 kb of the chlorella virus PBCV-1 330-kb genome: map positions 182 to 258." Kutish G.F., Li Y., Lu Z., Furuta M., Rock D.L., van Etten J.L. Virology 223:303-317(1996) [PubMed: 8806566] [Abstract] Cited for: NUCLEOTIDE SEQUENCE.
[5]	"Analysis of 74 kb of DNA located at the right end of the 330-kb chlorella virus PBCV-1 genome." Li Y., Lu Z., Sun L., Ropp S., Kutish G.F., Rock D.L., van Etten J.L. Virology 237:360-377(1997) [PubMed: 9356347] [Abstract] Cited for: NUCLEOTIDE SEQUENCE.
[6]	"Chlorella virus PBCV-1 encodes a functional homospermidine synthase." Kaiser A., Vollmert M., Tholl D., Graves M.V., Gurnon J.R., Xing W., Lisec A.D., Nickerson K.W., Van Etten J.L. Virology 263:254-262(1999) [PubMed: 10544099] [Abstract] Cited for: NUCLEOTIDE SEQUENCE.
[7]	"Characterization of a beta-1,3-glucanase encoded by chlorella virus PBCV-1." Sun L., Gurnon J.R., Adams B.J., Graves M.V., Van Etten J.L. Virology 276:27-36(2000) [PubMed: 11021991] [Abstract] Cited for: NUCLEOTIDE SEQUENCE.
[8]	"Microarray analysis of Paramecium bursaria chlorella virus 1 transcription." Yanai-Balser G.M., Duncan G.A., Eudy J.D., Wang D., Li X., Agarkova I.V., Dunigan D.D., Van Etten J.L. J. Virol. 84:532-542(2010) [PubMed: 19828609] [Abstract] Cited for: NUCLEOTIDE SEQUENCE.
[9]	"Paramecium bursaria Chlorella virus 1 proteome reveals novel architectural and regulatory features of a giant virus." Dunigan D.D., Blanc G., Duncan G.A., Gurnon J.R., Jeanniard A., McClung O.W., Upton C., Van Etten J.L. Submitted (FEB-2011) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE.
[10]	"Crystal structure of eukaryotic DNA ligase-adenylate illuminates the mechanism of nick sensing and strand joining." Odell M., Sriskanda V., Shuman S., Nikolov D.B. Mol. Cell 6:1183-1193(2000) [PubMed: 11106756] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 2-298 IN COMPLEX WITH AMP.
[11]	"Analysis of the DNA joining repertoire of Chlorella virus DNA ligase and a new crystal structure of the ligase-adenylate intermediate." Odell M., Malinina L., Sriskanda V., Teplova M., Shuman S. Nucleic Acids Res. 31:5090-5100(2003) [PubMed: 12930960] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.95 ANGSTROMS) IN COMPLEX WITH AMP.
[12]	"Structural basis for nick recognition by a minimal pluripotent DNA ligase." Nair P.A., Nandakumar J., Smith P., Odell M., Lima C.D., Shuman S. Nat. Struct. Mol. Biol. 14:770-778(2007) [PubMed: 17618295] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) IN COMPLEX WITH AMP.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

JF411744 Genomic DNA. Translation: AAC96909.1.

PIR

T18046.

RefSeq

NP_048900.1. NC_000852.5.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1FVI	X-ray	2.00	A	2-298	[»]
1P8L	X-ray	2.95	A	1-298	[»]
2Q2T	X-ray	2.30	A	1-298	[»]
2Q2U	X-ray	3.00	A/B/C/D	1-298	[»]

ProteinModelPortal

O41026.

ModBase

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Protocols and materials databases

StructuralBiologyKnowledgebase

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Genome annotation databases

GeneID

917798.

Phylogenomic databases

ProtClustDB

CLSP2494331.

Family and domain databases

InterPro

IPR012310. DNA_ligase_ATP-dep_cent.
IPR016059. DNA_ligase_ATP-dep_CS.
IPR012340. NA-bd_OB-fold.
IPR016027. NA-bd_OB-fold-like.
[Graphical view]

Gene3D

G3DSA:2.40.50.140. OB_NA_bd_sub. 1 hit.

Pfam

PF01068. DNA_ligase_A_M. 1 hit.
[Graphical view]

SUPFAM

SSF50249. Nucleic_acid_OB. 1 hit.

PROSITE

PS00333. DNA_LIGASE_A2. 1 hit.
[Graphical view]

ProtoNet

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Entry information

Entry name

O41026_PBCV1

Accession

Primary (citable) accession number: O41026

Entry history

Integrated into UniProtKB/TrEMBL:	January 1, 1998
Last sequence update:	January 1, 1998
Last modified:	October 19, 2011
This is version 72 of the entry and version 1 of the sequence. [Complete history]

Entry status

Unreviewed (UniProtKB/TrEMBL)