DNA gyrase subunit B - Mycobacterium smegmatis

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P0C559 (GYRB_MYCSM) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 32. History...

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

Documents (2) |

Third-party data

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

Names and origin

Protein names

Recommended name:
DNA gyrase subunit B
EC=5.99.1.3

Gene names

Name:

gyrB

Organism

Mycobacterium smegmatis

Taxonomic identifier

1772 [NCBI]

Taxonomic lineage

Bacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Corynebacterineae › Mycobacteriaceae › Mycobacterium

Protein attributes

Sequence length	675 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	DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings. HAMAP-Rule MF_01898
Catalytic activity	ATP-dependent breakage, passage and rejoining of double-stranded DNA. HAMAP-Rule MF_01898
Cofactor	Magnesium. Binds two Mg²⁺ per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn²⁺ and Ca²⁺ By similarity.
Subunit structure	Heterotetramer, composed of two GyrA and two GyrB chains. Within the heterotetramer, GyrA contains the active site tyrosine that forms a covalent intermediate with the DNA, while GyrB contributes the cofactor binding sites and catalyzes ATP hydrolysis By similarity.
Subcellular location	Cytoplasm Potential HAMAP-Rule MF_01898.
Sequence similarities	Belongs to the type II topoisomerase family. Contains 1 Toprim domain.
Sequence caution	The sequence CAA63253.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Cellular component	Cytoplasm
Ligand	ATP-binding DNA-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Isomerase Topoisomerase
Technical term	3D-structure
Gene Ontology (GO)
Biological_process	DNA topological change Inferred from electronic annotation. Source: InterPro DNA-dependent DNA replication Inferred from electronic annotation. Source: HAMAP
Cellular_component	chromosome Inferred from electronic annotation. Source: InterPro cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: HAMAP DNA topoisomerase type II (ATP-hydrolyzing) activity Inferred from electronic annotation. Source: HAMAP metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed By similarity

Chain

2 – 675

674

DNA gyrase subunit B HAMAP-Rule MF_01898

PRO_0000145324

Regions

Domain

453 – 567

115

Toprim

Sites

Metal binding

459

Magnesium 1; catalytic By similarity

Metal binding

532

Magnesium 1; catalytic By similarity

Metal binding

532

Magnesium 2 By similarity

Metal binding

534

Magnesium 2 By similarity

Site

484

Interaction with DNA By similarity

Site

487

Interaction with DNA By similarity

Experimental info

Sequence conflict

162

G → R in CAA58884. Ref.2

Secondary structure

675

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P0C559 [UniParc].

Last modified July 10, 2007. Version 1.
Checksum: 68A9B7F98BE07951
Show »

FASTA

675

74,512

        10         20         30         40         50         60 
MAAQKNNAPK EYGADSITIL EGLEAVRKRP GMYIGSTGER GLHHLIWEVV DNAVDEAMAG 

        70         80         90        100        110        120 
FATRVDVKIH ADGSVEVRDD GRGIPVEMHA TGMPTIDVVM TQLHAGGKFD GETYAVSGGL 

       130        140        150        160        170        180 
HGVGVSVVNA LSTRLEATVL RDGYEWFQYY DRSVPGKLKQ GGETKETGTT IRFWADPEIF 

       190        200        210        220        230        240 
ETTDYNFETV ARRLQEMAFL NKGLTIELTD ERVTAEEVVD DVVKDTAEAP KTADEKAAEA 

       250        260        270        280        290        300 
TGPSKVKHRV FHYPGGLVDY VKHINRTKTP IQQSIIDFDG KGPGHEVEIA MQWNAGYSES 

       310        320        330        340        350        360 
VHTFANTINT HEGGTHEEGF RAALTSVVNR YAKDKKLLKD KDPNLTGDDI REGLAAVISV 

       370        380        390        400        410        420 
KVAEPQFEGQ TKTKLGNTEV KSFVQKICNE QLQHWFEANP AEAKTVVNKA VSSAQARIAA 

       430        440        450        460        470        480 
RKARELVRRK SATDIGGLPG KLADCRSTDP SKSELYVVEG DSAGGSAKSG RDSMFQAILP 

       490        500        510        520        530        540 
LRGKIINVEK ARIDRVLKNT EVQSIITALG TGIHDEFDIS KLRYHKIVLM ADADVDGQHI 

       550        560        570        580        590        600 
STLLLTLLFR FMKPLVENGH IFLAQPPLYK LKWQRSEPEF AYSDRERDGL LEAGRAAGKK 

       610        620        630        640        650        660 
INVDDGIQRY KGLGEMDAKE LWETTMDPSV RVLRQVTLDD AAAADELFSI LMGEDVEARR 

       670 
SFITRNAKDV RFLDV

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References

[1]

"Organization of the origins of replication of the chromosomes of Mycobacterium smegmatis, Mycobacterium leprae and Mycobacterium tuberculosis and isolation of a functional origin from M. smegmatis."
Salazar L., Fsihi H., De Rossi E., Riccardi G., Rios C., Cole S.T., Takiff H.E.
Mol. Microbiol. 20:283-293(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 607 / DSM 43465 / JCM 20379 / NBRC 3207 / NRRL B-692.

[2]

"Mycobacterium smegmatis DNA gyrase: cloning and overexpression in Escherichia coli."
Madhusudan K., Nagaraja V.
Microbiology 141:3029-3037(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: SN2.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X92503 Genomic DNA. Translation: CAA63253.1. Different initiation.
X84077 Genomic DNA. Translation: CAA58884.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
4B6C	X-ray	2.20	A/B	9-212	[»]

ProteinModelPortal

P0C559.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

Gene3D

3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.

HAMAP

MF_01898. GyrB.

InterPro

IPR002288. DNA_gyrase_B_C.
IPR011557. GyrB.
IPR003594. HATPase_ATP-bd.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
IPR001241. Topo_IIA.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR013760. Topo_IIA_like_dom.
IPR018522. TopoIIA_CS.
IPR006171. Toprim_domain.
[Graphical view]

Pfam

PF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]

PRINTS

PR00418. TPI2FAMILY.

SMART

SM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view]

SUPFAM

SSF55874. ATP_bd_ATPase. 1 hit.
SSF54211. Ribosomal_S5_D2-typ_fold. 1 hit.
SSF56719. Topo_IIA_cen. 1 hit.

TIGRFAMs

TIGR01059. gyrB. 1 hit.

PROSITE

PS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

GYRB_MYCSM

Accession

Primary (citable) accession number: P0C559
Secondary accession number(s): P48355, Q59555

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 10, 2007
Last sequence update:	July 10, 2007
Last modified:	May 1, 2013
This is version 32 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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

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

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protocols and materials databases

Family and domain databases

Entry information

Relevant documents