P69486 (D_BPPHX) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
External scaffolding protein D
Short name=GPD

Gene names

Name:

D

Organism

Enterobacteria phage phiX174 (Bacteriophage phi-X174)

Taxonomic identifier

10847 [NCBI]

Taxonomic lineage

Viruses › ssDNA viruses › Microviridae › Microvirus

Virus host

Escherichia coli [TaxID: 562]

Protein attributes

Sequence length	152 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Assembles the procapsid by joining twelve 12S pre-assembly complex into a T=1 icosahedral particle, called 108S procapsid. Ten proteins D bind each 12S complex, which are formed by three pentamers of F, G, B protein and a H protein. The scaffolding protein is released from the provirion after genome packaging to form the mature virion. Ref.4 Ref.6
Subunit structure	Component of the procapsid particle composed of 60 copies of the internally located B, 240 copies of the external scaffolding protein D, 60 copies of each of the viral structural proteins F and G, and 12 copies of protein H.
Subcellular location	Host cytoplasm.
Sequence similarities	Belongs to the microvirus D protein family.

Ontologies

Keywords
Biological process	Capsid assembly
Cellular component	Host cytoplasm
Technical term	3D-structure
Gene Ontology (GO)
Biological process	viral procapsid maturation Inferred from electronic annotation. Source: InterPro
Cellular component	host cell cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed; by host

Chain

2 – 152

151

External scaffolding protein D

PRO_0000164880

Experimental info

Mutagenesis

61

1

G → D: Confers a lethal phenotype. Ref.5

Mutagenesis

61

1

G → E: Confers a lethal phenotype. Ref.5

Mutagenesis

61

1

G → V: Confers a lethal phenotype. Ref.5

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

152

Helix Strand Turn

Details...

Helix

5 – 23

19

Helix

31 – 38

8

Helix

48 – 59

12

Helix

61 – 65

5

Helix

75 – 85

11

Helix

88 – 97

10

Turn

98 – 100

3

Helix

104 – 109

6

Helix

117 – 129

13

Sequences

	Sequence		Length	Mass (Da)
	P69486 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: E8C912DCBA48D5E4	FASTA	152	16,937
	10 20 30 40 50 60 MSQVTEQSVR FQTALASIKL IQASAVLDLT EDDFDFLTSN KVWIATDRSR ARRCVEACVY 70 80 90 100 110 120 GTLDFVGYPR FPAPVEFIAA VIAYYVHPVN IQTACLIMEG AEFTENIING VERPVKAAEL 130 140 150 FAFTLRVRAG NTDVLTDAEE NVRQKLRAEG VM

References

[1]	"Nucleotide sequence of bacteriophage phi X174 DNA." Sanger F., Air G.M., Barrell B.G., Brown N.L., Coulson A.R., Fiddes J.C., Hutchison C.A. III, Slocombe P.M., Smith M. Nature 265:687-695(1977) [PubMed: 870828] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Overlapping genes in bacteriophage phiX174." Barrell B.G., Air G.M., Hutchison C.A. III Nature 264:34-41(1976) [PubMed: 1004533] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"Role of premature translational termination in the regulation of expression of the phi X174 lysis gene." Buckley K.J., Hayashi M. J. Mol. Biol. 198:599-607(1987) [PubMed: 2963134] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-68.
[4]	"Isolation and identification of bacteriophage phi X174 prohead." Mukai R., Hamatake R.K., Hayashi M. Proc. Natl. Acad. Sci. U.S.A. 76:4877-4881(1979) [PubMed: 159449] [Abstract] Cited for: FUNCTION AND PROCAPSID STRUCTURE.
[5]	"Genetic analyses of putative conformation switching and cross-species inhibitory domains in Microviridae external scaffolding proteins." Burch A.D., Fane B.A. Virology 310:64-71(2003) [PubMed: 12788631] [Abstract] Cited for: MUTAGENESIS OF GLY-61.
[6]	"Identification of an interacting coat-external scaffolding protein domain required for both the initiation of phiX174 procapsid morphogenesis and the completion of DNA packaging." Uchiyama A., Fane B.A. J. Virol. 79:6751-6756(2005) [PubMed: 15890913] [Abstract] Cited for: FUNCTION.
[7]	"Structure of a viral procapsid with molecular scaffolding." Dokland T., McKenna R., Ilag L.L., Bowman B.R., Incardona N.L., Fane B.A., Rossmann M.G. Nature 389:308-313(1997) [PubMed: 9305849] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.5 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J02482 Genomic DNA. Translation: AAA32575.1.
X07809 Genomic DNA. Translation: CAA30667.1.

PIR

ZDBPF4. A04245.

RefSeq

NP_040708.1. NC_001422.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1AL0	X-ray	3.50	1/2/3/4	1-152	[»]
1CD3	X-ray	3.50	1/2/3/4	1-151	[»]
1TX9	X-ray	3.31	A/B	2-152	[»]

ProteinModelPortal

P69486.

SMR

P69486. Positions 7-152.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

2546399.

GenomeReviews

Gene locus phiX174p08 in contig J02482_GR.

Phylogenomic databases

ProtClustDB

PHA0006.

Family and domain databases

InterPro

IPR004196. Scaffold_D_phage.
[Graphical view]

Gene3D

G3DSA:1.10.1850.10. Bact_scaffold_pD. 1 hit.

Pfam

PF02925. gpD. 1 hit.
[Graphical view]

ProDom

PD016331. Bact_scaffold_pD. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SUPFAM

SSF48045. Bact_scaffold_pD. 1 hit.

ProtoNet

Search...

Entry information

Entry name

D_BPPHX

Accession

Primary (citable) accession number: P69486
Secondary accession number(s): P03637

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	January 23, 2007
Last modified:	January 25, 2012
This is version 41 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program