DNA polymerase III subunit psi - Escherichia coli (strain K12)

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P28632 (HOLD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 112. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
DNA polymerase III subunit psi
EC=2.7.7.7

Gene names

Name:	holD
Ordered Locus Names:	b4372, JW4334

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	137 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The exact function of the psi subunit is unknown.
Catalytic activity	Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
Subunit structure	The DNA polymerase holoenzyme is a complex that contains 10 different types of subunits. These subunits are organized into 3 functionally essential subassemblies: the pol III core, the beta sliding clamp processivity factor and the clamp-loading complex. The pol III core (subunits alpha,epsilon and theta) contains the polymerase and the 3'-5' exonuclease proofreading activities. The polymerase is tethered to the template via the sliding clamp processivity factor. The clamp-loading complex assembles the beta processivity factor onto the primer template and plays a central role in the organization and communication at the replication fork. This complex contains delta, delta', psi and chi, and copies of either or both of two different DnaX proteins, gamma and tau. The composition of the holoenzyme is, therefore: (alpha,epsilon,theta)[2]-(gamma/tau)[3]-delta,delta', psi,chi-beta[4].

Ontologies

Keywords
Biological process	DNA replication
Molecular function	DNA-directed DNA polymerase Nucleotidyltransferase Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA replication Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	3'-5' exonuclease activity Inferred from electronic annotation. Source: InterPro DNA-directed DNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
dnaX	P06710	15	EBI-549176,EBI-549140
holC	P28905	13	EBI-549176,EBI-549169

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 137

137

DNA polymerase III subunit psi

PRO_0000105520

Secondary structure

137

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P28632 [UniParc].

Last modified December 1, 1992. Version 1.
Checksum: 5B7356201E7E27FE
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FASTA

137

15,174

        10         20         30         40         50         60 
MTSRRDWQLQ QLGITQWSLR RPGALQGEIA IAIPAHVRLV MVANDLPALT DPLVSDVLRA 

        70         80         90        100        110        120 
LTVSPDQVLQ LTPEKIAMLP QGSHCNSWRL GTDEPLSLEG AQVASPALTD LRANPTARAA 

       130 
LWQQICTYEH DFFPRND

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"DNA polymerase III accessory proteins. III. holC and holD encoding chi and psi." Xiao H., Crombie R., Dong Z., Onrust R., O'Donnell M. J. Biol. Chem. 268:11773-11778(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"Identification, isolation, and overexpression of the gene encoding the psi subunit of DNA polymerase III holoenzyme." Carter J.R., Franden M.A., Aebersold R.H., McHenry C.S. J. Bacteriol. 175:5604-5610(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"Cloning and nucleotide sequencing of the genes rimI and rimJ which encode enzymes acetylating ribosomal proteins S18 and S5 of Escherichia coli K12." Yoshikawa A., Isono S., Sheback A., Isono K. Mol. Gen. Genet. 209:481-488(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[4]	"Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes." Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R. Nucleic Acids Res. 23:2105-2119(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[6]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[7]	"DNA polymerase III accessory proteins. IV. Characterization of chi and psi." Xiao H., Dong Z., O'Donnell M. J. Biol. Chem. 268:11779-11784(1993) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION.
[8]	"Accessory protein function in the DNA polymerase III holoenzyme from E. coli." O'Donnell M. Bioessays 14:105-111(1992) [PubMed] [Europe PMC] [Abstract] Cited for: REVIEW.
[9]	"Crystal structure of the chi:psi sub-assembly of the Escherichia coli DNA polymerase clamp-loader complex." Gulbis J.M., Kazmirski S.L., Finkelstein J., Kelman Z., O'Donnell M., Kuriyan J. Eur. J. Biochem. 271:439-449(2004) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 26-137.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

L04575 Genomic DNA. Translation: AAA24435.1.
L05387 Unassigned DNA. Translation: AAA03076.1.
X06117 Genomic DNA. No translation available.
U14003 Genomic DNA. Translation: AAA97268.1.
U00096 Genomic DNA. Translation: AAC77325.1.
AP009048 Genomic DNA. Translation: BAE78360.1.

PIR

A48647.

RefSeq

NP_418789.1. NC_000913.2.
YP_492501.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1EM8	X-ray	2.10	B/D	26-137	[»]
3GLI	X-ray	3.50	O/P	2-28	[»]
3SXU	X-ray	1.85	B	2-137	[»]

ProteinModelPortal

P28632.

SMR

P28632. Positions 2-137.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-9934N.

IntAct

P28632. 22 interactions.

MINT

MINT-1224283.

STRING

511145.b4372.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC77325; AAC77325; b4372.
BAE78360; BAE78360; BAE78360.

GeneID

12933791.
948890.

KEGG

ecj:Y75_p4255.
eco:b4372.

PATRIC

32124354. VBIEscCol129921_4517.

Organism-specific databases

EchoBASE

EB1386.

EcoGene

EG11414. holD.

Phylogenomic databases

eggNOG

COG3050.

HOGENOM

HOG000218328.

K02344.

OMA

ITQWTLR.

ProtClustDB

PRK06856.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11414-MONOMER.
ECOL316407:JW4334-MONOMER.

Gene expression databases

Genevestigator

P28632.

Family and domain databases

Gene3D

3.40.50.10220. 1 hit.

InterPro

IPR004615. DNA_pol_III_psi.
IPR018382. DNA_pol_III_psi_subgr.
[Graphical view]

Pfam

PF03603. DNA_III_psi. 1 hit.
[Graphical view]

PIRSF

PIRSF029225. DNA_pol_III_psi. 1 hit.

ProDom

PD032475. DNA_pol_III_psi. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SUPFAM

SSF102220. DNA_pol_III_psi. 1 hit.

TIGRFAMs

TIGR00664. DNA_III_psi. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P28632.

Entry information

Entry name

HOLD_ECOLI

Accession

Primary (citable) accession number: P28632
Secondary accession number(s): Q2M5U6

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 1, 1992
Last sequence update:	December 1, 1992
Last modified:	May 1, 2013
This is version 112 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents