Conserved Protein Domain Family

cd05403: NT_KNTase_like 
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Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins.
S. aureus KNTase is a plasmid encoded enzyme which confers resistance to a wide range of aminoglycoside antibiotics which have a 4'- or 4''-hydroxyl group in the equatorial position, such as kanamycin A. This enzyme transfers a nucleoside monophosphate group from a nucleotide (ATP,GTP, or UTP) to the 4'-hydroxyl group of kanamycin A. This enzyme is a homodimer, having two NT active sites. The nucleotide and antibiotic binding sites of each active site include residues from each monomer. Included in this subgroup is Escherichia coli AadA5 which confers resistance to the antibiotic spectinomycin and is a putative aminoglycoside-3'-adenylyltransferase. It is part of the aadA5 cassette of a class 1 integron. This subgroup also includes Haemophilus influenzae HI0073 which forms a 2:2 heterotetramer with an unrelated protein HI0074. Structurally HI0074 is related to the substrate-binding domain of S. aureus KNTase. The genes encoding HI0073 and HI0074 form an operon. Little is known about the substrate specificity or function of two-component NTs. The characterized members of this subgroup may not be representive of the function of this subgroup. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, co-ordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These carboxylate residues are conserved in this subgroup.
PSSM-Id: 143393
View PSSM: cd05403
Aligned: 328 rows
Threshold Bit Score: 35.4703
Threshold Setting Gi: 62423904
Created: 25-Jul-2007
Updated: 17-Jan-2013
Aligned Rows:
Conserved site includes 9 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
  • Comment:based on similarity to Staphylococcus aureus KNTase.
  • Structure:1KNY_A, Staphylococcus aureus KNTase homodimer, bound with Mg2+-AMP-CPP (an ATP analog) and kanamycin A, contacts determined at 4A.
    View structure with Cn3D
  • Comment:Staphylococcus aureus KNTase is homodimeric, with two active sites in the dimer. Both monomers contribute residues to each NTP and antibiotic binding site. Other members of this group such as HI0073, the NT domain of HI0073/ HI0074 (a two-component NT), displays a different dimer association than that of Staphylococcus aureus KNTase.
  • Citation:PMID 7577914

Sequence Alignment
Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
Feature 1                                    ###  #      ## #                           # #      
1KNY_A        13 MKIVHEIKERILDKygd----dvKAIGVYGSLGRQTdgpySDIEMMCVmsteeaefs------hewttgewKVEVNFYse 82
gi 56421246   11 RTVFRQLLHLFSRYad-----viEKVILFGSRARGDykegSDIDLAIQfrkpggplyll-qsdldelpiiyPIDVVDYnq 84
gi 28211092    4 DKLKTQLEKIFAKYpq------vEKVVLFGSRARGDnkynSDIDLCIFgeelshltlakitfyiedldtclMFDILAFne 77
gi 20808391   18 VSLLGEIIKVLSKYes------vEKAVIFGSRGRGDfkrtSDIDICVFgekithtelnllqfdleglntplSFDVVHFdt 91
gi 119720320  16 RRFFESYVERIVGFfg-----grVTLILFGSRARGDemlsSDYDLAVVveeevdvlglt-etlvkmrprglPVDVVVLqk 89
gi 156862673   6 DNELEKLCNLFRKHee------iEQAVLYGSRAKGNfkpfSDIDITLMgdrltyntlsslsdeiddlllpySVDLSIYgk 79
gi 126466438  10 ARRMKSWEEGFKEFvsvlcmdnvLEAYLVGSRARGDylpySDYDVVVIvressdpleea-vrlrrlrkhsfPLDLIVLtp 88
gi 15921339   20 LELYKNEETQFKEYvsyl-cernYTVILFGSRARGDykiySDYDLLVIgeem---------------pklpPTDAIELhf 83
gi 78188572    8 DSHLHIIRSIFKQYqa------iNKVLIYGSRAKGNyserSDVDLVICdttfdrktigkillainnsdfpyTVDLQIMen 81
gi 114330203   9 QAAITRLCHIFSQYpq------iDSVILYGSRAKGNyrpgSDIDLSIQgeqldlttllaienqiddlllpwMVDLSLFhk 82
                         90       100
Feature 1                                     
1KNY_A        83 eilldyasqv--esdwplthgqfFSILPI 109
gi 56421246   85 ihneq------------lkmnidQEGKTI 101
gi 28211092   78 ltkkdl----------iknilneGVVIYR 96
gi 20808391   92 lcrke------------fresilKDGVEI 108
gi 119720320  90 eelgdplvt---rmltpcrmlynGLGIQE 115
gi 156862673  80 lknadl----------lehihrmGIPIFS 98
gi 126466438  89 sqasd-----------piydemfRTAIKL 106
gi 15921339   84 vkkekledkirefntividafyeGKVICD 112
gi 78188572   82 iknkn------------lqehikRVGKEF 98
gi 114330203  83 idnpd-----------liehiqrIGIPFY 100

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