DNA gyrase subunit B - Mycobacterium ulcerans (strain Agy99)

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A0PKB6 (A0PKB6_MYCUA) Unreviewed, UniProtKB/TrEMBL

Last modified May 1, 2013. Version 54. History...

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

Third-party data

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

Names and origin

Protein names

Recommended name:
DNA gyrase subunit B RuleBase RU003363 HAMAP-Rule MF_01898
EC=5.99.1.3 RuleBase RU003363 HAMAP-Rule MF_01898

Gene names

Name:	gyrB HAMAP-Rule MF_01898 EMBL ABL02785.1
Ordered Locus Names:	MUL_0005 EMBL ABL02785.1

Organism

Mycobacterium ulcerans (strain Agy99) [Complete proteome] [HAMAP] EMBL ABL02785.1

Taxonomic identifier

362242 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	692 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

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 By similarity. RuleBase RU003363 HAMAP-Rule MF_01898
Catalytic activity	ATP-dependent breakage, passage and rejoining of double-stranded DNA. RuleBase RU003363 HAMAP-Rule MF_01898 SAAS SAAS011557
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. HAMAP-Rule MF_01898
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. HAMAP-Rule MF_01898
Subcellular location	Cytoplasm By similarity HAMAP-Rule MF_01898.
Sequence similarities	Belongs to the type II topoisomerase family. HAMAP-Rule MF_01898 RuleBase RU000380 Contains 1 Toprim domain. HAMAP-Rule MF_01898 SAAS SAAS011557

Ontologies

Keywords
Cellular component	Cytoplasm HAMAP-Rule MF_01898
Ligand	ATP-binding HAMAP-Rule MF_01898 RuleBase RU000380 SAAS SAAS011557 DNA-binding HAMAP-Rule MF_01898 Magnesium HAMAP-Rule MF_01898 Metal-binding HAMAP-Rule MF_01898 Nucleotide-binding
Molecular function	Isomerase Topoisomerase HAMAP-Rule MF_01898 RuleBase RU000380 SAAS SAAS011557
Technical term	Complete proteome
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

Regions

Domain

470 – 584

115

Toprim By similarity HAMAP-Rule MF_01898

Sites

Metal binding

476

Magnesium 1; catalytic By similarity HAMAP-Rule MF_01898

Metal binding

549

Magnesium 1; catalytic By similarity HAMAP-Rule MF_01898

Metal binding

549

Magnesium 2 By similarity HAMAP-Rule MF_01898

Metal binding

551

Magnesium 2 By similarity HAMAP-Rule MF_01898

Site

501

Interaction with DNA By similarity HAMAP-Rule MF_01898

Site

504

Interaction with DNA By similarity HAMAP-Rule MF_01898

Sequences

Sequence

Length

Mass (Da)

Tools

A0PKB6 [UniParc].

Last modified January 9, 2007. Version 1.
Checksum: 122507FC19548B79
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FASTA

692

76,125

        10         20         30         40         50         60 
MTGPRASNPE ENIRTVAAQK KKAQDEYGAS AITVLEGLEA VRKRPGMYIG STGERGLHHL 

        70         80         90        100        110        120 
VWEVVDNSVD EAMAGYATQV NVRLLDDGSV EVADNGRGIP VAMHATGAPT VDVVMTQLHA 

       130        140        150        160        170        180 
GGKFGGENSG YNVSGGLHGV GVSVVNALST RLEVDIKRDG YEWSQFYDRA QPGTLKQGEA 

       190        200        210        220        230        240 
TKKTGTAIRF WADPDIFETT EYDFETVARR LQEMAFLNKG LTINLTDERV TPDEVVDDVV 

       250        260        270        280        290        300 
SDTAEAPKSA QEKAAESTAP HKVKSRTFHY PGGLVDFVKH INRTKSPIQQ SIVDFEGKGS 

       310        320        330        340        350        360 
GHEVEIAMQW NGGYSESVHT FANTINTHEG GTHEEGFRSA LTSVVNKYAK DKKLLKDKDP 

       370        380        390        400        410        420 
NLTGDDIREG LAAVISVRVA EPQFEGQTKT KLGNTEVKSF VQKVCNEQLT HWFEANPSEA 

       430        440        450        460        470        480 
KTIVNKAVSS AQARLAARKA RELVRRKSAT DLGGLPGKLA DCRSTDPRKS ELYVVEGDSA 

       490        500        510        520        530        540 
GGSAKSGRDS MFQAILPLRG KIINVEKARI DRVLKNTEVQ AIITALGTGI HDEFDLSKLR 

       550        560        570        580        590        600 
YHKIVLMADA DVDGQHISTL LLTLLFRFMR PLIENGHVFL AQPPLYKLKW QRTEPEFAYS 

       610        620        630        640        650        660 
DRERDGLLEA GLKAGKKINK EDGIQRYKGL GEMDAKELWE TTMDPSVRVL RQVTLDDAAA 

       670        680        690 
ADELFSILMG EDVDARRSFI TRNAKDVRFL DV

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References

[1]

"Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer."
Stinear T.P., Seemann T., Pidot S.J.A., Frigui W., Reysset G., Garnier T., Meurice G., Simon D., Bouchier C., Ma L., Tichit M., Porter J.L., Ryan J.E., Johnson P.D.R., Davies J.K., Jenkin G.A., Small P.L.C., Jones L.M.

Cole S.T.
Genome Res. 17:192-200(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: Agy99 EMBL ABL02785.1.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000325 Genomic DNA. Translation: ABL02785.1.
RefSeq	YP_904256.1. NC_008611.1.
3D structure databases
ProteinModelPortal	A0PKB6.
ModBase	Search...
Protein-protein interaction databases
STRING	362242.MUL_0005.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	ABL02785; ABL02785; MUL_0005.
GeneID	4553249.
KEGG	mul:MUL_0005.
PATRIC	18166432. VBIMycUlc37413_0098.
Organism-specific databases
GenoList	MUL_0005.
CMR	Search...
Phylogenomic databases
eggNOG	COG0187.
HOGENOM	HOG000075154.
KO	K02470.
OMA	IFETTEF.
ProtClustDB	PRK05644.
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. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

A0PKB6_MYCUA

Accession

Primary (citable) accession number: A0PKB6

Entry history

Integrated into UniProtKB/TrEMBL:	January 9, 2007
Last sequence update:	January 9, 2007
Last modified:	May 1, 2013
This is version 54 of the entry and version 1 of the sequence. [Complete history]

Entry status

Unreviewed (UniProtKB/TrEMBL)

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

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Regions

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Family and domain databases

Entry information