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Protein

Type-2 restriction enzyme BamHI

Gene

bamHIR

Organism
Bacillus amyloliquefaciens (Bacillus velezensis)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Recognizes the double-stranded sequence GGATCC and cleaves after G-1.1 Publication

Catalytic activityi

Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.2 Publications

Cofactori

Mg2+Note: Binds 2 magnesium ions per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi77 – 771Magnesium 2
Active sitei94 – 941
Metal bindingi94 – 941Magnesium 1
Metal bindingi94 – 941Magnesium 2
Active sitei111 – 1111
Metal bindingi112 – 1121Magnesium 1; via carbonyl oxygen
Active sitei113 – 1131

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

Restriction system

Keywords - Ligandi

Magnesium, Metal-binding

Protein family/group databases

REBASEi185. BamHI.

Names & Taxonomyi

Protein namesi
Recommended name:
Type-2 restriction enzyme BamHI (EC:3.1.21.42 Publications)
Short name:
R.BamHI
Alternative name(s):
Endonuclease BamHI
Type II restriction enzyme BamHI
Gene namesi
Name:bamHIR
OrganismiBacillus amyloliquefaciens (Bacillus velezensis)
Taxonomic identifieri1390 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 213213Type-2 restriction enzyme BamHIPRO_0000077281Add
BLAST

Interactioni

Subunit structurei

Homodimer.

Structurei

Secondary structure

1
213
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 87Combined sources
Helixi10 – 189Combined sources
Helixi20 – 3415Combined sources
Beta strandi43 – 486Combined sources
Helixi58 – 614Combined sources
Helixi62 – 709Combined sources
Beta strandi75 – 784Combined sources
Helixi81 – 844Combined sources
Beta strandi87 – 893Combined sources
Beta strandi93 – 1019Combined sources
Beta strandi104 – 1129Combined sources
Helixi117 – 13216Combined sources
Beta strandi137 – 1448Combined sources
Helixi146 – 1494Combined sources
Helixi159 – 1624Combined sources
Helixi163 – 1697Combined sources
Beta strandi174 – 1807Combined sources
Beta strandi182 – 1854Combined sources
Helixi200 – 2056Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1BAMX-ray1.95A1-213[»]
1BHMX-ray2.20A/B1-213[»]
1ESGX-ray1.90A/B1-213[»]
2BAMX-ray2.00A/B1-213[»]
3BAMX-ray1.80A/B1-213[»]
ProteinModelPortaliP23940.
SMRiP23940. Positions 1-212.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP23940.

Family & Domainsi

Family and domain databases

Gene3Di3.40.91.20. 1 hit.
InterProiIPR011338. BamHI/BglII/BstY.
IPR011335. Restrct_endonuc-II-like.
IPR004194. Restrct_endonuc_II_BamHI.
[Graphical view]
PfamiPF02923. BamHI. 1 hit.
[Graphical view]
PIRSFiPIRSF009309. Restrict_endonuc_II_BamHI. 1 hit.
SUPFAMiSSF52980. SSF52980. 1 hit.

Sequencei

Sequence statusi: Complete.

P23940-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEVEKEFITD EAKELLSKDK LIQQAYNEVK TSICSPIWPA TSKTFTINNT
60 70 80 90 100
EKNCNGVVPI KELCYTLLED TYNWYREKPL DILKLEKKKG GPIDVYKEFI
110 120 130 140 150
ENSELKRVGM EFETGNISSA HRSMNKLLLG LKHGEIDLAI ILMPIKQLAY
160 170 180 190 200
YLTDRVTNFE ELEPYFELTE GQPFIFIGFN AEAYNSNVPL IPKGSDGMSK
210
RSIKKWKDKV ENK
Length:213
Mass (Da):24,570
Last modified:March 1, 1992 - v1
Checksum:iFFE57F518F37D8D6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X55285 Genomic DNA. Translation: CAA38999.1.
PIRiA38693.
S26844.
RefSeqiWP_013353547.1. NG_034330.1.
YP_009073767.1. NG_034330.1.

Genome annotation databases

GeneIDi9779203.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X55285 Genomic DNA. Translation: CAA38999.1.
PIRiA38693.
S26844.
RefSeqiWP_013353547.1. NG_034330.1.
YP_009073767.1. NG_034330.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1BAMX-ray1.95A1-213[»]
1BHMX-ray2.20A/B1-213[»]
1ESGX-ray1.90A/B1-213[»]
2BAMX-ray2.00A/B1-213[»]
3BAMX-ray1.80A/B1-213[»]
ProteinModelPortaliP23940.
SMRiP23940. Positions 1-212.
ModBaseiSearch...
MobiDBiSearch...

Chemistry

BindingDBiP23940.
ChEMBLiCHEMBL5928.

Protein family/group databases

REBASEi185. BamHI.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi9779203.

Miscellaneous databases

EvolutionaryTraceiP23940.

Family and domain databases

Gene3Di3.40.91.20. 1 hit.
InterProiIPR011338. BamHI/BglII/BstY.
IPR011335. Restrct_endonuc-II-like.
IPR004194. Restrct_endonuc_II_BamHI.
[Graphical view]
PfamiPF02923. BamHI. 1 hit.
[Graphical view]
PIRSFiPIRSF009309. Restrict_endonuc_II_BamHI. 1 hit.
SUPFAMiSSF52980. SSF52980. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Characterization of the cloned BamHI restriction modification system: its nucleotide sequence, properties of the methylase, and expression in heterologous hosts."
    Brooks J.E., Nathan P.D., Landry D., Sznyter L.A., White-Rees P., Ives C.L., Moran L.S., Slatko B.E., Benner J.S.
    Nucleic Acids Res. 19:841-850(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-8 AND 11-14.
    Strain: ATCC 49763 / H.
  2. "Isolation of a sequence-specific endonuclease (BamI) from Bacillus amyloliquefaciens H."
    Wilson G.A., Young F.E.
    J. Mol. Biol. 97:123-125(1975) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS AN ENDONUCLEASE, CATALYTIC ACTIVITY.
    Strain: ATCC 49763 / H / RUB500.
  3. "Recognition sequence of specific endonuclease BamH.I from Bacillus amyloliquefaciens H."
    Roberts R.J., Wilson G.A., Young F.E.
    Nature 265:82-84(1977) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBSTRATE SPECIFICITY, CATALYTIC ACTIVITY.
    Strain: ATCC 49763 / H.
  4. "Structure of restriction endonuclease BamHI and its relationship to EcoRI."
    Newman M., Strzelecka T., Dorner L.F., Schildkraut I., Aggarwal A.K.
    Nature 368:660-664(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS).
  5. "The role of metals in catalysis by the restriction endonuclease BamHI."
    Viadiu H., Aggarwal A.K.
    Nat. Struct. Biol. 5:910-916(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).

Entry informationi

Entry nameiT2BA_BACAM
AccessioniPrimary (citable) accession number: P23940
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 1992
Last sequence update: March 1, 1992
Last modified: May 27, 2015
This is version 96 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, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Restriction enzymes and methylases
    Classification of restriction enzymes and methylases and list of entries

External Data

Dasty 3

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 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.