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E1C9K5 (E1C9K5_GEOSE) Unreviewed, UniProtKB/TrEMBL

Last modified June 11, 2014. Version 28. 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 namesRecommended name:
DNA polymerase RuleBase RU004460

EC=2.7.7.7 RuleBase RU004460
OrganismGeobacillus stearothermophilus (Bacillus stearothermophilus) PDB 2XO7
Taxonomic identifier1422 [NCBI]
Taxonomic lineageBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus

Protein attributes

Sequence length580 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Catalytic activity

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).

Sequence similarities

Belongs to the DNA polymerase type-A family. RuleBase RU004459

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Regions

Region10 – 134Sulfate 3 binding
Region25 – 262Sulfate 4 binding PDB 4B9S PDB 4B9U PDB 4B9V
Region76 – 794Sucrose binding PDB 2XY7 PDB 4B9L PDB 4B9N PDB 4B9S
Region234 – 2374Sulfate 8 binding
Region359 – 3602Sulfate 10 binding PDB 2XO7 PDB 4B9M PDB 4B9N
Region371 – 3733Sulfate 11 binding PDB 4B9M PDB 4B9V
Region449 – 4524Sulfate 11 binding PDB 4B9M PDB 4B9V

Sites

Metal binding581Calcium PDB 4DSK
Metal binding601Calcium PDB 4DSK
Metal binding3571Magnesium PDB 4B9M PDB 4B9S PDB 4B9V
Metal binding3581Magnesium; via carbonyl oxygen PDB 4B9M PDB 4B9S PDB 4B9V
Metal binding5341Magnesium PDB 4B9M PDB 4B9S PDB 4B9V
Binding site41Sulfate 1; via amide nitrogen PDB 2XY6 PDB 2Y1J PDB 4DSI PDB 4DSL PDB 4B9L PDB 4B9M PDB 4B9V
Binding site41Sulfate 2; via amide nitrogen PDB 2XO7
Binding site261Sulfate 5; via carbonyl oxygen PDB 4B9N
Binding site291Sucrose PDB 2XY7 PDB 4B9L PDB 4B9N PDB 4B9S
Binding site471Sulfate 1 PDB 2XY5 PDB 2XY6 PDB 2Y1J PDB 4DSI PDB 4B9S
Binding site471Sulfate 2 PDB 2XO7 PDB 2XY7 PDB 2Y1I
Binding site1121Sucrose; via carbonyl oxygen PDB 2XY7 PDB 4B9L PDB 4B9N PDB 4B9S
Binding site1291Sulfate 4 PDB 4B9S PDB 4B9U PDB 4B9V
Binding site1291Sulfate 5 PDB 4B9N
Binding site1291Sulfate 6 PDB 2XY5
Binding site1291Sulfate 7 PDB 4B9M
Binding site3111Sucrose PDB 2XY7 PDB 4B9L PDB 4B9N PDB 4B9S
Binding site3361Sulfate 9; via carbonyl oxygen PDB 4B9L
Binding site3811Sulfate 12 PDB 4B9N PDB 4B9T PDB 4B9U
Binding site4061Sulfate 13 PDB 2XY5 PDB 2XY6 PDB 2Y1I PDB 2Y1J PDB 4DSI PDB 4DSL PDB 4B9L PDB 4B9M PDB 4B9N PDB 4B9T
Binding site4061Sulfate 14 PDB 2XO7
Binding site4101Sulfate 13 PDB 2XY5 PDB 2XY6 PDB 2Y1I PDB 2Y1J PDB 4DSI PDB 4DSL PDB 4B9L PDB 4B9M PDB 4B9N PDB 4B9T
Binding site4101Sulfate 14 PDB 2XO7
Binding site4831Sulfate 16 PDB 2XO7 PDB 2XY5 PDB 4B9L PDB 4B9M PDB 4B9N PDB 4B9S PDB 4B9U PDB 4B9V
Binding site4931Sulfate 15 PDB 4DSI
Binding site5231Sulfate 17 PDB 2XY7

Sequences

Sequence LengthMass (Da)Tools
E1C9K5 [UniParc].

Last modified November 2, 2010. Version 1.
Checksum: 355FFB1153F1B829

FASTA58066,131
        10         20         30         40         50         60 
AKMAFTLADR VTEEMLADKA ALVVEVVEEN YHDAPIVGIA VVNEHGRFFL RPETALADPQ 

        70         80         90        100        110        120 
FVAWLGDETK KKSMFDSKRA AVALKWKGIE LCGVSFDLLL AAYLLDPAQG VDDVAAAAKM 

       130        140        150        160        170        180 
KQYEAVRPDE AVYGKGAKRA VPDEPVLAEH LVRKAAAIWA LERPFLDELR RNEQDRLLVE 

       190        200        210        220        230        240 
LEQPLSSILA EMEFAGVKVD TKRLEQMGEE LAEQLRTVEQ RIYELAGQEF NINSPKQLGV 

       250        260        270        280        290        300 
ILFEKLQLPV LKKSKTGYST SADVLEKLAP YHEIVENILH YRQLGKLQST YIEGLLKVVR 

       310        320        330        340        350        360 
PDTKKVHTIF NQALTQTGRL SSTEPNLQNI PIRLEEGRKI RQAFVPSESD WLIFAADYSQ 

       370        380        390        400        410        420 
IELRVLAHIA EDDNLMEAFR RDLDIHTKTA MDIFQVSEDE VTPNMRRQAK AVNFGIVYGI 

       430        440        450        460        470        480 
SDYGLAQNLN ISRKEAAEFI ERYFESFPGV KRYMENIVQE AKQKGYVTTL LHRRRYLPDI 

       490        500        510        520        530        540 
TSRNFNVRSF AERMAMNTPI QGSAADIIKK AMIDLNARLK EERLQARLLL QVHDELILEA 

       550        560        570        580 
PKEEMERLCR LVPEVMEQAV TLRVPLKVDY HYGSTWYDAK 

« Hide

References

[1]"Chemical discrimination between dC and 5MedC via their hydroxylamine adducts."
Munzel M., Lercher L., Muller M., Carell T.
Nucleic Acids Res. 38:e192-e192(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS) IN COMPLEX WITH SULFATE.
[2]"Crystal structures and repair studies reveal the identity and the base-pairing properties of the UV-induced spore photoproduct DNA lesion."
Heil K., Kneuttinger A.C., Schneider S., Lischke U., Carell T.
Chemistry 17:9651-9657(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) IN COMPLEX WITH SULFATE.
[3]"Reversible bond formation enables the replication and amplification of a crosslinking salen complex as an orthogonal base pair."
Kaul C., Muller M., Wagner M., Schneider S., Carell T.
Nat. Chem. 3:794-800(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.22 ANGSTROMS) IN COMPLEX WITH SUCROSE AND SULFATE.
[4]"Biochemical and structural insights into the fidelity of bacillus stearothermophilus DNA polymerase."
Gan J.H., Abdur R., Liu H.H., Sheng J., Caton-Willians J., Soares A.S., Huang Z.
Submitted (FEB-2012) to the PDB data bank
Cited for: X-RAY CRYSTALLOGRAPHY (2.86 ANGSTROMS) OF 2-580.
[5]"Unexpected non-Hoogsteen-based mutagenicity mechanism of FaPy-DNA lesions."
Gehrke T.H., Lischke U., Gasteiger K.L., Schneider S., Arnold S., Muller H.C., Stephenson D.S., Zipse H., Carell T.
Nat. Chem. Biol. 9:455-461(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.73 ANGSTROMS) IN COMPLEX WITH MAGNESIUM; SUCROSE AND SULFATE.

Cross-references

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2XO7X-ray2.85A1-580[»]
2XY5X-ray2.22A1-580[»]
2XY6X-ray2.30A1-580[»]
2XY7X-ray3.05A1-580[»]
2Y1IX-ray2.78A1-580[»]
2Y1JX-ray2.15A1-580[»]
4B9LX-ray2.05A1-580[»]
4B9MX-ray2.05A1-580[»]
4B9NX-ray2.20A1-580[»]
4B9SX-ray1.73A1-580[»]
4B9TX-ray2.65A1-580[»]
4B9UX-ray2.10A1-580[»]
4B9VX-ray2.00A1-580[»]
4DSIX-ray2.05A2-580[»]
4DSJX-ray2.86A/B2-580[»]
4DSKX-ray2.18A2-580[»]
4DSLX-ray2.45A2-580[»]
4DWIX-ray1.85A2-580[»]
ProteinModelPortalE1C9K5.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

Gene3D3.30.420.10. 1 hit.
InterProIPR002562. 3'-5'_exonuclease_dom.
IPR019760. DNA-dir_DNA_pol_A_CS.
IPR001098. DNA-dir_DNA_pol_A_palm_dom.
IPR018320. DNA_polymerase_1.
IPR002298. DNA_polymerase_A.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamPF00476. DNA_pol_A. 1 hit.
[Graphical view]
PRINTSPR00868. DNAPOLI.
SMARTSM00474. 35EXOc. 1 hit.
SM00482. POLAc. 1 hit.
[Graphical view]
SUPFAMSSF53098. SSF53098. 1 hit.
TIGRFAMsTIGR00593. pola. 1 hit.
PROSITEPS00447. DNA_POLYMERASE_A. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceE1C9K5.

Entry information

Entry nameE1C9K5_GEOSE
AccessionPrimary (citable) accession number: E1C9K5
Entry history
Integrated into UniProtKB/TrEMBL: November 2, 2010
Last sequence update: November 2, 2010
Last modified: June 11, 2014
This is version 28 of the entry and version 1 of the sequence. [Complete history]
Entry statusUnreviewed (UniProtKB/TrEMBL)