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A3DJ38 (A3DJ38_CLOTH) Unreviewed, UniProtKB/TrEMBL

Last modified June 11, 2014. Version 61. Feed History...

Clusters with 100%, 90%, 50% identity | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein names
Gene names
Ordered Locus Names:Cthe_2768 EMBL ABN53967.1
OrganismClostridium thermocellum (strain ATCC 27405 / DSM 1237) [Complete proteome] [HAMAP] EMBL ABN53967.1
Taxonomic identifier203119 [NCBI]
Taxonomic lineageBacteriaFirmicutesClostridiaClostridialesClostridiaceaeClostridium

Protein attributes

Sequence length870 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Regions

Nucleotide binding17 – 237ATP PDB 4GP7
Nucleotide binding17 – 237CTP PDB 4JT2
Nucleotide binding17 – 237GTP PDB 4JSY PDB 4MDF
Nucleotide binding18 – 236ADP PDB 4GP6
Nucleotide binding120 – 1234ATP PDB 4GP7
Nucleotide binding120 – 1234CTP PDB 4JT2
Nucleotide binding120 – 1234GTP PDB 4JSY PDB 4MDF
Nucleotide binding495 – 4962ADP PDB 3TY5
Nucleotide binding529 – 5324AMP PDB 3TY9 PDB 4E6N
Region187 – 1893Citrate 3 binding PDB 4J6O
Region263 – 2642Citrate 3 binding PDB 4J6O

Sites

Metal binding1871Manganese
Metal binding1891Manganese; via tele nitrogen
Metal binding2331Manganese
Metal binding7311Magnesium; via carbonyl oxygen PDB 3TY9
Metal binding7341Magnesium; via carbonyl oxygen PDB 3TY9
Metal binding7371Magnesium; via carbonyl oxygen PDB 3TY9
Binding site621Citrate 1 PDB 4MDF
Binding site661Citrate 1 PDB 4MDF
Binding site1161ADP PDB 4GP6
Binding site1161ATP PDB 4GP7
Binding site1161CTP PDB 4JT2
Binding site1161GTP PDB 4JSY PDB 4MDF
Binding site1201ADP PDB 4GP6
Binding site1621GTP PDB 4JSY
Binding site2331Citrate 3 PDB 4J6O
Binding site2371Citrate 3 PDB 4J6O
Binding site3231Citrate 3 PDB 4J6O
Binding site3761Citrate 3; via carbonyl oxygen PDB 4J6O
Binding site5311ATP PDB 3TY5
Binding site5361ADP PDB 3TY5
Binding site5361AMP PDB 3TY9 PDB 4E6N
Binding site5361ATP PDB 3TY5
Binding site5651ADP PDB 3TY5
Binding site5651ATP PDB 3TY5
Binding site6071ADP PDB 3TY5
Binding site6071AMP PDB 3TY9 PDB 4E6N
Binding site6071ATP PDB 3TY5
Binding site6871AMP PDB 3TY9
Binding site7041ADP PDB 3TY5
Binding site7041AMP PDB 3TY9 PDB 4E6N
Binding site7041ATP PDB 3TY5
Binding site7691AMP PDB 3TY9
Binding site7741ADP PDB 3TY5
Binding site7741AMP PDB 3TY9 PDB 4E6N
Binding site7741ATP PDB 3TY5
Binding site7921ADP PDB 3TY5
Binding site7921AMP PDB 3TY9 PDB 4E6N
Binding site7921ATP PDB 3TY5
Binding site8241ADP PDB 3TY5

Sequences

Sequence LengthMass (Da)Tools
A3DJ38 [UniParc].

Last modified March 20, 2007. Version 1.
Checksum: 11CA5878DD2919E9

FASTA87098,776
        10         20         30         40         50         60 
MKLTIPELSL VVLIGSSGSG KSTFAKKHFK PTEVISSDFC RGLVSDDEND QTVTGAAFDV 

        70         80         90        100        110        120 
LHYIVSKRLQ LGKLTVVDAT NVQESARKPL IEIAKDYHCF PVAVVFNLPE KVCQERNKNR 

       130        140        150        160        170        180 
TDRQVEEYVI RKHTQQLKKS IKGLQREGFR YVYILNSPEE VEEVVFERQP LWNNKKDEHG 

       190        200        210        220        230        240 
PFDIIGDIHG CYDELKMLLE KLGYLIEEVE GGVGSGKYRV THPEGRKVLF LGDLVDRGPK 

       250        260        270        280        290        300 
ITEVLKLVMG MVKSGIALCV PGNHDVKLLR KLNGRDVQIT HGLDRTLEQL AKEPQEFIEE 

       310        320        330        340        350        360 
VKAFIDGLVS HYVLDDGKLV VAHAGMKEEF QGRGSGKVRE FALYGETTGE TDEYGLPVRY 

       370        380        390        400        410        420 
DWASDYRGKA LVVYGHTPQA EVLKVNNTIN IDTGCVFGGK LTAYRYPERE IVDVKALKTY 

       430        440        450        460        470        480 
YEPAKPFLPK EDMAERFEAR TDNDILDIND VLGKKIITTR LMSSITIHEE NSIAALEVMS 

       490        500        510        520        530        540 
RFAADPHWLI YLPPTMSPCE TSKKEGMLEH PIEAFEYFRT RGVGKVVCEQ KHMGSRAVVI 

       550        560        570        580        590        600 
VCKDSQVAEK RFGVLDGTAG ICYTRTGRHF FDDMQLEAEL IDRVRKVLDK SGFWGDFNTD 

       610        620        630        640        650        660 
WVCLDCELMP WSAKAQKLLE EQYSAVGISG RVVLDEAVKL LKQASLNKTV SFDVSRQTSG 

       670        680        690        700        710        720 
KNADINELLQ RFTERSEMMQ KYVEAYRKYC WPVNSIDDLK LAPFHILATE GKVHSDKNHI 

       730        740        750        760        770        780 
WHMDTIAKYC TQDDSLIMAT NHILVDVTDA ESVDKGIKWW EDLTASGGEG MVVKPYDFIV 

       790        800        810        820        830        840 
KNGRELLQPA VKCRGREYLR IIYGPEYTMD ENIERLRNRA VGKKRSLALR EFSLGMEALE 

       850        860        870 
RFVRNEPLYR VHECVFGVLA LESEPVDPRL 

« Hide

References

« Hide 'large scale' references
[1]"Complete sequence of Clostridium thermocellum ATCC 27405."
US DOE Joint Genome Institute
Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Chertkov O., Brettin T., Bruce D., Han C., Tapia R., Gilna P., Schmutz J. expand/collapse author list , Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Wu J.H.D., Newcomb M., Richardson P.
Submitted (FEB-2007) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 27405 / DSM 1237.
[2]"The adenylyltransferase domain of bacterial Pnkp defines a unique RNA ligase family."
Smith P., Wang L.K., Nair P.A., Shuman S.
Proc. Natl. Acad. Sci. U.S.A. 109:2296-2301(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) OF 479-870 IN COMPLEX WITH ADP; AMP; ATP AND MAGNESIUM.
[3]"Molecular basis of bacterial protein Hen1 activating the ligase activity of bacterial protein Pnkp for RNA repair."
Wang P., Chan C.M., Christensen D., Zhang C., Selvadurai K., Huang R.H.
Proc. Natl. Acad. Sci. U.S.A. 109:13248-13253(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.39 ANGSTROMS) OF 445-870 IN COMPLEX WITH AMP.
[4]"Structure and mechanism of the polynucleotide kinase component of the bacterial Pnkp-Hen1 RNA repair system."
Wang L.K., Das U., Smith P., Shuman S.
RNA 18:2277-2286(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 1-170 IN COMPLEX WITH ADP AND ATP.
[5]"Structural and biochemical analysis of the phosphate donor specificity of the polynucleotide kinase component of the bacterial pnkp.hen1 RNA repair system."
Das U., Wang L.K., Smith P., Shuman S.
Biochemistry 52:4734-4743(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.01 ANGSTROMS) OF 1-170 IN COMPLEX WITH CTP AND GTP.
[6]"Structure and mechanism of the 2',3' phosphatase component of the bacterial Pnkp-Hen1 RNA repair system."
Wang L.K., Smith P., Shuman S.
Nucleic Acids Res. 41:5864-5873(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF 171-424 IN COMPLEX WITH CITRATE AND MANGANESE.
[7]"Structures of bacterial polynucleotide kinase in a Michaelis complex with GTP.Mg2+ and 5'-OH oligonucleotide and a product complex with GDP.Mg2+ and 5'-PO4 oligonucleotide reveal a mechanism of general acid-base catalysis and the determinants of phosphoacceptor recognition."
Das U., Wang L.K., Smith P., Jacewicz A., Shuman S.
Nucleic Acids Res. 42:1152-1161(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.73 ANGSTROMS) OF 1-170 IN COMPLEX WITH CITRATE AND GTP.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP000568 Genomic DNA. Translation: ABN53967.1.
RefSeqYP_001039160.1. NC_009012.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3TY5X-ray2.40A/B479-870[»]
3TY8X-ray2.60A/B479-870[»]
3TY9X-ray3.12A/B/C/D479-870[»]
4DRFX-ray2.60A/C445-870[»]
4E6NX-ray2.39A/C445-870[»]
4GP6X-ray2.10A/B1-170[»]
4GP7X-ray2.00A/B1-170[»]
4J6OX-ray1.60A/B171-424[»]
4JSTX-ray2.03A/B1-170[»]
4JSYX-ray2.14A/B1-170[»]
4JT2X-ray2.49A/B1-170[»]
4JT4X-ray2.01A/B1-170[»]
4MDEX-ray1.80A/B1-170[»]
4MDFX-ray1.73A/B1-170[»]
ProteinModelPortalA3DJ38.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-60067N.
STRING203119.Cthe_2768.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaABN53967; ABN53967; Cthe_2768.
GeneID4810085.
KEGGcth:Cthe_2768.
PATRIC19519588. VBICloThe47081_2947.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0639.
HOGENOMHOG000245786.
KOK01090.
OMAHGCRSEL.
OrthoDBEOG6WX4P8.

Enzyme and pathway databases

BioCycCTHE203119:GIW8-2869-MONOMER.

Family and domain databases

Gene3D3.40.50.300. 1 hit.
3.60.21.10. 1 hit.
InterProIPR004843. Calcineurin-like_PHP_apaH.
IPR029052. Metallo-depent_PP-like.
IPR027417. P-loop_NTPase.
IPR024028. PNKP_bac.
IPR006186. Ser/Thr-sp_prot-phosphatase.
[Graphical view]
PfamPF00149. Metallophos. 1 hit.
[Graphical view]
PRINTSPR00114. STPHPHTASE.
SMARTSM00156. PP2Ac. 1 hit.
[Graphical view]
SUPFAMSSF52540. SSF52540. 1 hit.
SSF56300. SSF56300. 1 hit.
TIGRFAMsTIGR04075. bacter_Pnkp. 1 hit.
ProtoNetSearch...

Entry information

Entry nameA3DJ38_CLOTH
AccessionPrimary (citable) accession number: A3DJ38
Entry history
Integrated into UniProtKB/TrEMBL: March 20, 2007
Last sequence update: March 20, 2007
Last modified: June 11, 2014
This is version 61 of the entry and version 1 of the sequence. [Complete history]
Entry statusUnreviewed (UniProtKB/TrEMBL)