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Protein

Bacterial dynamin-like protein

Gene

Npun_R6513

Organism
Nostoc punctiforme (strain ATCC 29133 / PCC 73102)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Dynamin-related GTPase probably involved in membrane remodeling. Lipid and nucleotide-binding are thought to induce a large intramolecular rearrangement, leading to assembly on lipid bilayers and possible membrane curving. In the presence of the non-hydrolyzable GTP analog GMP-PNP self-assembles on a lipid bilayer; this does not stimulate subsequent GTPase activity. Does not bind lipids in the presence of GDP; perhaps GTP hydrolysis disrupts membrane-binding.1 Publication

Catalytic activityi

GTP + H2O = GDP + phosphate.

Kineticsi

kcat 0.53/min.

  1. KM=68.6 µM for GTP1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi79 – 846GTP
    Nucleotide bindingi235 – 2417GTP
    Nucleotide bindingi292 – 2932GTP

    GO - Molecular functioni

    • GTPase activity Source: UniProtKB
    • GTP binding Source: UniProtKB
    • lipid binding Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Ligandi

    GTP-binding, Lipid-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciNPUN63737:GJNP-6379-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Bacterial dynamin-like protein (EC:3.6.5.5)
    Short name:
    BDLP
    Gene namesi
    Ordered Locus Names:Npun_R6513
    OrganismiNostoc punctiforme (strain ATCC 29133 / PCC 73102)
    Taxonomic identifieri63737 [NCBI]
    Taxonomic lineageiBacteriaCyanobacteriaNostocalesNostocaceaeNostoc
    Proteomesi
    • UP000001191 Componenti: Chromosome

    Subcellular locationi

    • Cell membrane 1 Publication; Multi-pass membrane protein 1 Publication

    • Note: Probably inserts into the outer leaflet of the membrane only (Probable). Forms foci localized in the cell periphery, and occasionally in the cell interior.Curated

    Topology

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Topological domaini1 – 521521CytoplasmicSequence analysisAdd
    BLAST
    Transmembranei522 – 54221Discontinuously helicalSequence analysisAdd
    BLAST
    Topological domaini543 – 55311In membraneSequence analysisAdd
    BLAST
    Transmembranei554 – 57421Discontinuously helicalSequence analysisAdd
    BLAST
    Topological domaini575 – 693119CytoplasmicSequence analysisAdd
    BLAST

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cell membrane, Membrane

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi82 – 821K → A: 15-fold reduction of GTP hydrolysis. 1 Publication
    Mutagenesisi576 – 5772LL → EE: No lipid-binding. 1 Publication
    Mutagenesisi583 – 5831F → E: No lipid-binding. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 693693Bacterial dynamin-like proteinPRO_0000425573Add
    BLAST

    Expressioni

    Developmental stagei

    Detected in vegetatively growing cells (at protein level).1 Publication

    Interactioni

    Subunit structurei

    Homodimer. Self-assembles in the presence of GMP-PNP and liposomes, and probably also in the presence of GTP.1 Publication

    Protein-protein interaction databases

    DIPiDIP-60443N.
    STRINGi63737.Npun_R6513.

    Structurei

    Secondary structure

    1
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi6 – 3934Combined sources
    Turni40 – 467Combined sources
    Helixi52 – 6716Combined sources
    Beta strandi70 – 756Combined sources
    Helixi82 – 909Combined sources
    Turni101 – 1033Combined sources
    Beta strandi107 – 1115Combined sources
    Beta strandi116 – 1249Combined sources
    Beta strandi129 – 1313Combined sources
    Helixi132 – 1387Combined sources
    Helixi143 – 1508Combined sources
    Turni151 – 1533Combined sources
    Beta strandi160 – 1678Combined sources
    Helixi170 – 1734Combined sources
    Beta strandi175 – 1806Combined sources
    Helixi184 – 1885Combined sources
    Helixi191 – 1944Combined sources
    Helixi196 – 1994Combined sources
    Beta strandi200 – 20910Combined sources
    Helixi216 – 22510Combined sources
    Turni226 – 2283Combined sources
    Beta strandi233 – 2386Combined sources
    Helixi240 – 2467Combined sources
    Beta strandi247 – 2493Combined sources
    Helixi253 – 27119Combined sources
    Helixi272 – 2754Combined sources
    Beta strandi276 – 2794Combined sources
    Helixi283 – 2853Combined sources
    Beta strandi287 – 2893Combined sources
    Helixi292 – 30110Combined sources
    Helixi312 – 32514Combined sources
    Helixi327 – 35731Combined sources
    Helixi362 – 3709Combined sources
    Helixi372 – 40938Combined sources
    Turni410 – 4156Combined sources
    Helixi416 – 4194Combined sources
    Turni420 – 4223Combined sources
    Helixi428 – 4325Combined sources
    Helixi436 – 49762Combined sources
    Helixi516 – 5227Combined sources
    Beta strandi527 – 5348Combined sources
    Beta strandi536 – 5383Combined sources
    Helixi544 – 55310Combined sources
    Turni559 – 5613Combined sources
    Helixi562 – 57817Combined sources
    Turni579 – 5824Combined sources
    Helixi586 – 65570Combined sources
    Helixi660 – 69334Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2J68X-ray3.10A1-693[»]
    2J69X-ray3.00A/B/C/D1-693[»]
    2W6Delectron microscopy9.00A/B1-693[»]
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiB2IZD3.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini66 – 313248Dynamin-type GAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni68 – 287220GTPase domainAdd
    BLAST
    Regioni311 – 571261Middle domainAdd
    BLAST
    Regioni572 – 60635Paddle domainAdd
    BLAST
    Regioni607 – 69387GEDAdd
    BLAST

    Coiled coil

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Coiled coili347 – 37832Sequence analysisAdd
    BLAST
    Coiled coili661 – 68828Sequence analysisAdd
    BLAST

    Domaini

    The GTPase domain dimerizes and forms the BDLP tube surface, the middle and GED domains are elongated and involved in self-assembly, while the paddle region inserts into the outer leaflet of the membrane, possibly promoting membrane curvature.2 Publications

    Sequence similaritiesi

    Keywords - Domaini

    Coiled coil, Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiENOG410890F. Bacteria.
    COG0699. LUCA.
    HOGENOMiHOG000035501.
    OMAiNCHAILF.
    OrthoDBiEOG6P8TJ9.
    PhylomeDBiB2IZD3.

    Family and domain databases

    Gene3Di3.40.50.300. 1 hit.
    InterProiIPR022812. Dynamin_SF.
    IPR030381. G_DYNAMIN_dom.
    IPR027417. P-loop_NTPase.
    [Graphical view]
    PfamiPF00350. Dynamin_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF52540. SSF52540. 1 hit.
    PROSITEiPS51718. G_DYNAMIN_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    B2IZD3-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MVNQVATDRF IQDLERVAQV RSEMSVCLNK LAETINKAEL AGDSSSGKLS
    60 70 80 90 100
    LERDIEDITI ASKNLQQGVF RLLVLGDMKR GKSTFLNALI GENLLPSDVN
    110 120 130 140 150
    PCTAVLTVLR YGPEKKVTIH FNDGKSPQQL DFQNFKYKYT IDPAEAKKLE
    160 170 180 190 200
    QEKKQAFPDV DYAVVEYPLT LLQKGIEIVD SPGLNDTEAR NELSLGYVNN
    210 220 230 240 250
    CHAILFVMRA SQPCTLGERR YLENYIKGRG LTVFFLVNAW DQVRESLIDP
    260 270 280 290 300
    DDVEELQASE NRLRQVFNAN LAEYCTVEGQ NIYDERVFEL SSIQALRRRL
    310 320 330 340 350
    KNPQADLDGT GFPKFMDSLN TFLTRERAIA ELRQVRTLAR LACNHTREAV
    360 370 380 390 400
    ARRIPLLEQD VNELKKRIDS VEPEFNKLTG IRDEFQKEII NTRDTQARTI
    410 420 430 440 450
    SESFRSYVLN LGNTFENDFL RYQPELNLFD FLSSGKREAF NAALQKAFEQ
    460 470 480 490 500
    YITDKSAAWT LTAEKDINAA FKELSRSASQ YGASYNQITD QITEKLTGKD
    510 520 530 540 550
    VKVHTTTTAE EDNSPGWAKW AMGLLSLSKG NLAGFALAGA GFDWKNILLN
    560 570 580 590 600
    YFTVIGIGGI ITAVTGILLG PIGFALLGLG VGFLQADQAR RELVKTAKKE
    610 620 630 640 650
    LVKHLPQVAH EQSQVVYNAV KECFDSYERE VSKRINDDIV SRKSELDNLV
    660 670 680 690
    KQKQTREINR ESEFNRLKNL QEDVIAQLQK IEAAYSNLLA YYS
    Length:693
    Mass (Da):78,348
    Last modified:June 10, 2008 - v1
    Checksum:iDC1483C71AF1D80D
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    CP001037 Genomic DNA. Translation: ACC84775.1.
    RefSeqiWP_012412711.1. NC_010628.1.

    Genome annotation databases

    EnsemblBacteriaiACC84775; ACC84775; Npun_R6513.
    KEGGinpu:Npun_R6513.
    PATRICi22767045. VBINosPun48114_7640.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    CP001037 Genomic DNA. Translation: ACC84775.1.
    RefSeqiWP_012412711.1. NC_010628.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2J68X-ray3.10A1-693[»]
    2J69X-ray3.00A/B/C/D1-693[»]
    2W6Delectron microscopy9.00A/B1-693[»]
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-60443N.
    STRINGi63737.Npun_R6513.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiACC84775; ACC84775; Npun_R6513.
    KEGGinpu:Npun_R6513.
    PATRICi22767045. VBINosPun48114_7640.

    Phylogenomic databases

    eggNOGiENOG410890F. Bacteria.
    COG0699. LUCA.
    HOGENOMiHOG000035501.
    OMAiNCHAILF.
    OrthoDBiEOG6P8TJ9.
    PhylomeDBiB2IZD3.

    Enzyme and pathway databases

    BioCyciNPUN63737:GJNP-6379-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiB2IZD3.

    Family and domain databases

    Gene3Di3.40.50.300. 1 hit.
    InterProiIPR022812. Dynamin_SF.
    IPR030381. G_DYNAMIN_dom.
    IPR027417. P-loop_NTPase.
    [Graphical view]
    PfamiPF00350. Dynamin_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF52540. SSF52540. 1 hit.
    PROSITEiPS51718. G_DYNAMIN_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 29133 / PCC 73102.
    2. "A bacterial dynamin-like protein."
      Low H.H., Lowe J.
      Nature 444:766-769(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS) OF APOPROTEIN AND IN COMPLEX WITH GTP ANALOG, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE, DOMAIN, GTP-BINDING, LIPID-BINDING, MUTAGENESIS OF LYS-82.
      Strain: ATCC 29133 / PCC 73102.
    3. "Structure of a bacterial dynamin-like protein lipid tube provides a mechanism for assembly and membrane curving."
      Low H.H., Sachse C., Amos L.A., Lowe J.
      Cell 139:1342-1352(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY ELECTRON MICROSCOPY (9.00 ANGSTROMS) BOUND TO LIPID TUBES, DOMAIN, LIPID-BINDING, MUTAGENESIS OF 576-LEU-LEU-577 AND PHE-583.

    Entry informationi

    Entry nameiBDLP_NOSP7
    AccessioniPrimary (citable) accession number: B2IZD3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 19, 2014
    Last sequence update: June 10, 2008
    Last modified: April 13, 2016
    This is version 50 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    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.