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Protein

DDE-recombinase A

Gene

A

Organism
Enterobacteria phage Mu (Bacteriophage Mu)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Responsible for viral genome integration into the host chromosome. During integration of the incoming virus, DDE-recombinase A cleaves both viral DNA ends and the resulting 3'-OH perform a nucleophilic attack of the host DNA. The 5' flanking DNA attached to the ends of the viral genome (flaps) are resected by the DDE-recombinase A endonuclease activity, with the help of host chaperone ClpX. The gaps created in the host chromosome by the viral genome insertion are repaired by the host primary machinery for double-strand break repair.
Responsible for replication of the viral genome by replicative transposition. During replicative transposition, DDE-recombinase A is part of the transpososome complex. DDE-recombinase A cleaves the viral DNA and the resulting 3'-OH performs a nucleophilic attack of the host DNA. The 5' flanking DNA is not resected and an intermediary structure is formed. This structure is resolved by target-primed replication leading to two copies of the viral genome (the original one and the copied one). Host ClpX and translation initiation factor IF2 play an essential transpososome-remodeling role by releasing the block between transposition and DNA replication. Successive rounds of replicative transposition can lead up to 100 copies of the viral genome.
Promotes replication and thereby lytic development by competing with repressor c (Repc) for binding to the internal activation sequence (IAS) in the enhancer/operator region. The outcome of this competition determines if the virus enters latency or starts replication.

Cofactori

Mg2+2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi269Magnesium; catalytic1
Metal bindingi336Magnesium; catalyticCurated1
Metal bindingi392Magnesium; catalytic1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi176 – 196H-T-H motif; viral genome ends bindingPROSITE-ProRule annotationAdd BLAST21

GO - Molecular functioni

  • DNA binding Source: UniProtKB-KW
  • double-stranded DNA endodeoxyribonuclease activity Source: CACAO
  • ligase activity Source: UniProtKB-KW
  • metal ion binding Source: UniProtKB-KW
  • transposase activity Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Ligase, Nuclease

Keywords - Biological processi

DNA excision, DNA integration, DNA recombination, DNA replication, Transposition, Viral DNA replication

Keywords - Ligandi

DNA-binding, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
DDE-recombinase A (EC:3.1.22.-, EC:6.5.1.-)
Alternative name(s):
DDE-transposase A
Gene product 03
Short name:
gp03
Gene product A
Short name:
gpA
MuA
Gene namesi
Name:A
Ordered Locus Names:Mup03
OrganismiEnterobacteria phage Mu (Bacteriophage Mu)
Taxonomic identifieri10677 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stageCaudoviralesMyoviridaeMulikevirus
Virus hostiEnterobacteriaceae [TaxID: 543]
Proteomesi
  • UP000002611 Componenti: Genome

Subcellular locationi

GO - Cellular componenti

  • host Source: UniProtKB
  • host cell cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Host cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi269D → N: Complete loss of both the DNA cleavage and joining activities without bloing tetramer assembly. 2 Publications1
Mutagenesisi269D → V: Loss of DNA-protein assembly. 2 Publications1
Mutagenesisi294D → N: Almost complete loss of both the DNA cleavage and joining activities without bloing tetramer assembly. 2 Publications1
Mutagenesisi348G → D: Loss of DNA-protein assembly. 1 Publication1
Mutagenesisi392E → A: Complete loss of both the DNA cleavage and joining activities without bloing tetramer assembly. 2 Publications1
Mutagenesisi392E → Q: Complete loss of both the DNA cleavage and joining activities without bloing tetramer assembly. 2 Publications1
Mutagenesisi550D → N: Almost no effect on both the DNA cleavage and joining activities without bloing tetramer assembly. 1 Publication1
Mutagenesisi556E → Q: Almost no effect on both the DNA cleavage and joining activities without bloing tetramer assembly. 1 Publication1
Mutagenesisi558E → Q: Almost no effect on both the DNA cleavage and joining activities without bloing tetramer assembly. 1 Publication1
Mutagenesisi567D → N: Almost no effect on both the DNA cleavage and joining activities without bloing tetramer assembly. 1 Publication1
Mutagenesisi573E → Q: Almost no effect on both the DNA cleavage and joining activities without bloing tetramer assembly. 1 Publication1
Mutagenesisi575 – 579RRRQK → KKKQR: No effect on DNA-binding and flaps endonuclease activity. 1 Publication5
Mutagenesisi575 – 579RRRQK → LQLQQ: Almost complete loss of flaps endonuclease activity, DNA-binding and transpososome assembly. 1 Publication5
Mutagenesisi576 – 579RRQK → QRQQ: Partial loss of flaps endonuclease activity resulting in delayed flaps removal. Complete loss of DNA-binding. 4
Mutagenesisi596D → N: Almost no effect on both the DNA cleavage and joining activities without bloing tetramer assembly. 1 Publication1
Mutagenesisi599E → Q: Almost no effect on both the DNA cleavage and joining activities without bloing tetramer assembly. 1 Publication1
Mutagenesisi602E → Q: Almost no effect on both the DNA cleavage and joining activities without bloing tetramer assembly. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000775841 – 663DDE-recombinase AAdd BLAST663

Expressioni

Inductioni

Expressed in the early phase of the viral replicative cycle. Expression of early genes is repressed by viral Repc (latency) and favored by viral Ner protein.1 Publication

Keywords - Developmental stagei

Early protein

Interactioni

Subunit structurei

Homotetramer. Part of the transpososome complex composed of a DDE-recombinase A tetramer synapsing the ends of the viral genome and the enhancer element. Interacts with target DNA activator B; this interaction brings DDE-recombinase A to the transposition target site. Interacts with host ClpX; this interaction remodels the transpososome for replication and is required for the flaps endonuclease activity of DDE-recombinase A. Binds (via N-terminus) three distinct recognition sites in the AttR and AttL regions of the viral genome ends: R1, R2, and R3 on the right end and L1, L2, and L3 on the left, not all of which are essential for transposition. The active transpososome is formed by three DDE-recombinase A subunits tightly bound to R1, R2, L1 plus a fourth subunit tightly bound in the complex but weakly bound to the L2 recognition site. Only two subunits out of the four involved are responsible for catalysis. Each subunit performs the cleavage and joining reactions for one DNA end and acts in trans, ensuring the reaction is only initiated when both viral genome ends are paired.4 Publications

Protein-protein interaction databases

DIPiDIP-59984N.

Structurei

Secondary structure

1663
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi7 – 10Combined sources4
Beta strandi14 – 16Combined sources3
Helixi20 – 28Combined sources9
Beta strandi40 – 43Combined sources4
Turni50 – 52Combined sources3
Helixi55 – 64Combined sources10
Beta strandi69 – 72Combined sources4
Helixi90 – 98Combined sources9
Helixi101 – 122Combined sources22
Helixi127 – 137Combined sources11
Beta strandi138 – 140Combined sources3
Helixi142 – 153Combined sources12
Helixi157 – 165Combined sources9
Helixi182 – 192Combined sources11
Helixi200 – 214Combined sources15
Helixi221 – 231Combined sources11
Helixi233 – 240Combined sources8
Turni262 – 264Combined sources3
Beta strandi265 – 272Combined sources8
Beta strandi288 – 294Combined sources7
Turni295 – 297Combined sources3
Beta strandi300 – 308Combined sources9
Helixi311 – 325Combined sources15
Beta strandi327 – 330Combined sources4
Beta strandi332 – 334Combined sources3
Beta strandi338 – 340Combined sources3
Turni341 – 346Combined sources6
Turni351 – 354Combined sources4
Helixi363 – 370Combined sources8
Beta strandi373 – 375Combined sources3
Beta strandi377 – 379Combined sources3
Turni381 – 383Combined sources3
Helixi393 – 395Combined sources3
Helixi397 – 402Combined sources6
Turni403 – 406Combined sources4
Helixi408 – 410Combined sources3
Turni411 – 413Combined sources3
Helixi424 – 426Combined sources3
Turni427 – 429Combined sources3
Helixi433 – 449Combined sources17
Turni456 – 461Combined sources6
Helixi464 – 472Combined sources9
Helixi482 – 487Combined sources6
Beta strandi489 – 492Combined sources4
Beta strandi501 – 507Combined sources7
Beta strandi514 – 519Combined sources6
Helixi521 – 523Combined sources3
Beta strandi525 – 527Combined sources3
Beta strandi529 – 535Combined sources7
Helixi537 – 539Combined sources3
Turni540 – 542Combined sources3
Beta strandi543 – 547Combined sources5
Beta strandi553 – 559Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1BCMX-ray2.80A/B248-574[»]
1BCOX-ray2.40A248-574[»]
1TNSNMR-A1-76[»]
1TNTNMR-A1-76[»]
2EZHNMR-A174-247[»]
2EZINMR-A174-247[»]
2EZKNMR-A77-174[»]
2EZLNMR-A77-174[»]
4FCYX-ray3.71A/B77-605[»]
ProteinModelPortaliP07636.
SMRiP07636.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP07636.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 69HTH Mu-type; 1-alpha, viral IAS bindingPROSITE-ProRule annotationAdd BLAST69

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni77 – 1741-beta, viral genome ends bindingAdd BLAST98
Regioni175 – 2471-gamma, viral genome ends bindingAdd BLAST73
Regioni249 – 490CatalyticAdd BLAST242
Regioni491 – 605Target DNA capture and bendingAdd BLAST115
Regioni575 – 579Involved in flaps endonuclease activity5
Regioni605 – 663Interaction with MuBAdd BLAST59
Regioni656 – 663Interaction with and host ClpX8

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi269 – 392DDEAdd BLAST124

Domaini

The catalytic domain contains two distinct activities, the cleavage and strand transfer activity and the flaps endonuclease activity. The N-terminal HTH Mu-type domain 1-alpha is responsible for sequence-specific DNA binding to the IAS. Two adjacent regions 1-beta and 1-gamma bind to the ends of the viral genome.
Contains a D-x(n)-D-x(35)-E motif, named for the conserved glutamic acid and aspartic acid residues and the invariant 35 amino acid spacing between the second and third acidic residues. These residues coordinate the metal ions required for nucleophile activation. Each acidic residue of the D,D(35)E motif is independently essential for the 3'-processing and strand transfer activities (By similarity).By similarity

Sequence similaritiesi

Contains 1 HTH Mu-type domain.Curated

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
1.10.10.60. 2 hits.
2.30.30.130. 1 hit.
3.30.420.10. 1 hit.
InterProiIPR009061. DNA-bd_dom_put.
IPR009057. Homeodomain-like.
IPR003314. Mu-type_HTH.
IPR015126. Mu_I-gamma.
IPR004189. Phage_Mu_transposase.
IPR012337. RNaseH-like_dom.
IPR015378. Transposase-like_Mu_C.
IPR009004. Transposase_Mu_C.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF02914. DDE_2. 1 hit.
PF02316. HTH_Tnp_Mu_1. 1 hit.
PF09039. HTH_Tnp_Mu_2. 1 hit.
PF09299. Mu-transpos_C. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 2 hits.
SSF46955. SSF46955. 1 hit.
SSF50610. SSF50610. 1 hit.
SSF53098. SSF53098. 1 hit.
PROSITEiPS51702. HTH_MU. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P07636-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MELWVSPKEC ANLPGLPKTS AGVIYVAKKQ GWQNRTRAGV KGGKAIEYNA
60 70 80 90 100
NSLPVEAKAA LLLRQGEIET SLGYFEIARP TLEAHDYDRE ALWSKWDNAS
110 120 130 140 150
DSQRRLAEKW LPAVQAADEM LNQGISTKTA FATVAGHYQV SASTLRDKYY
160 170 180 190 200
QVQKFAKPDW AAALVDGRGA SRRNVHKSEF DEDAWQFLIA DYLRPEKPAF
210 220 230 240 250
RKCYERLELA AREHGWSIPS RATAFRRIQQ LDEAMVVACR EGEHALMHLI
260 270 280 290 300
PAQQRTVEHL DAMQWINGDG YLHNVFVRWF NGDVIRPKTW FWQDVKTRKI
310 320 330 340 350
LGWRCDVSEN IDSIRLSFMD VVTRYGIPED FHITIDNTRG AANKWLTGGA
360 370 380 390 400
PNRYRFKVKE DDPKGLFLLM GAKMHWTSVV AGKGWGQAKP VERAFGVGGL
410 420 430 440 450
EEYVDKHPAL AGAYTGPNPQ AKPDNYGDRA VDAELFLKTL AEGVAMFNAR
460 470 480 490 500
TGRETEMCGG KLSFDDVFER EYARTIVRKP TEEQKRMLLL PAEAVNVSRK
510 520 530 540 550
GEFTLKVGGS LKGAKNVYYN MALMNAGVKK VVVRFDPQQL HSTVYCYTLD
560 570 580 590 600
GRFICEAECL APVAFNDAAA GREYRRRQKQ LKSATKAAIK AQKQMDALEV
610 620 630 640 650
AELLPQIAEP AAPESRIVGI FRPSGNTERV KNQERDDEYE TERDEYLNHS
660
LDILEQNRRK KAI
Length:663
Mass (Da):75,003
Last modified:February 1, 1996 - v2
Checksum:iB882CFDCBFC0B2E3
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti66G → R in CAA24236 (PubMed:6222246).Curated1
Sequence conflicti408P → S in AAA32379 (Ref. 2) Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M11195 Genomic DNA. Translation: AAA32369.1.
M64097 Genomic DNA. Translation: AAA32379.1.
AF083977 Genomic DNA. Translation: AAF01083.1.
V01464 Genomic DNA. Translation: CAA24713.1.
V00868 Genomic DNA. Translation: CAA24236.1.
PIRiA24746. TQBPU.
RefSeqiNP_050607.1. NC_000929.1.

Genome annotation databases

GeneIDi2636292.
KEGGivg:2636292.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M11195 Genomic DNA. Translation: AAA32369.1.
M64097 Genomic DNA. Translation: AAA32379.1.
AF083977 Genomic DNA. Translation: AAF01083.1.
V01464 Genomic DNA. Translation: CAA24713.1.
V00868 Genomic DNA. Translation: CAA24236.1.
PIRiA24746. TQBPU.
RefSeqiNP_050607.1. NC_000929.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1BCMX-ray2.80A/B248-574[»]
1BCOX-ray2.40A248-574[»]
1TNSNMR-A1-76[»]
1TNTNMR-A1-76[»]
2EZHNMR-A174-247[»]
2EZINMR-A174-247[»]
2EZKNMR-A77-174[»]
2EZLNMR-A77-174[»]
4FCYX-ray3.71A/B77-605[»]
ProteinModelPortaliP07636.
SMRiP07636.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-59984N.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi2636292.
KEGGivg:2636292.

Miscellaneous databases

EvolutionaryTraceiP07636.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
1.10.10.60. 2 hits.
2.30.30.130. 1 hit.
3.30.420.10. 1 hit.
InterProiIPR009061. DNA-bd_dom_put.
IPR009057. Homeodomain-like.
IPR003314. Mu-type_HTH.
IPR015126. Mu_I-gamma.
IPR004189. Phage_Mu_transposase.
IPR012337. RNaseH-like_dom.
IPR015378. Transposase-like_Mu_C.
IPR009004. Transposase_Mu_C.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF02914. DDE_2. 1 hit.
PF02316. HTH_Tnp_Mu_1. 1 hit.
PF09039. HTH_Tnp_Mu_2. 1 hit.
PF09299. Mu-transpos_C. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 2 hits.
SSF46955. SSF46955. 1 hit.
SSF50610. SSF50610. 1 hit.
SSF53098. SSF53098. 1 hit.
PROSITEiPS51702. HTH_MU. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiTNPA_BPMU
AccessioniPrimary (citable) accession number: P07636
Secondary accession number(s): P06021
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: February 1, 1996
Last modified: November 2, 2016
This is version 126 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

This enzyme is structurally similar to and performs the same endonucleotidic reaction as retroviral integrases, RNase H, RuvC holliday resolvases and RAG proteins.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome, Transposable element

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.