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
Aligned: 328 rows
Threshold Bit Score: 35.4703
Created: 25-Jul-2007
Updated: 2-Oct-2020
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:
Feature 1                                    ###  #      ## #                           # #      
1KNY_A        13 MKIVHEIKERILDKygd----dvKAIGVYGSLGRQTdgpySDIEMMCVmsteeaefs------hewttgewKVEVNFYse 82  Staphylococcus ...
YP_148564     11 RTVFRQLLHLFSRYad-----viEKVILFGSRARGDykegSDIDLAIQfrkpggplyll-qsdldelpiiyPIDVVDYnq 84  Geobacillus kau...
NP_782036      4 DKLKTQLEKIFAKYpq------vEKVVLFGSRARGDnkynSDIDLCIFgeelshltlakitfyiedldtclMFDILAFne 77  Clostridium tet...
NP_623562     18 VSLLGEIIKVLSKYes------vEKAVIFGSRGRGDfkrtSDIDICVFgekithtelnllqfdleglntplSFDVVHFdt 91  Thermoanaerobac...
YP_920815     16 RRFFESYVERIVGFfg-----grVTLILFGSRARGDemlsSDYDLAVVveeevdvlglt-etlvkmrprglPVDVVVLqk 89  Thermofilum pen...
EDO56104       6 DNELEKLCNLFRKHee------iEQAVLYGSRAKGNfkpfSDIDITLMgdrltyntlsslsdeiddlllpySVDLSIYgk 79  Bacteroides uni...
YP_001041547  10 ARRMKSWEEGFKEFvsvlcmdnvLEAYLVGSRARGDylpySDYDVVVIvressdpleea-vrlrrlrkhsfPLDLIVLtp 88  Staphylothermus...
NP_377008     20 LELYKNEETQFKEYvsyl-cernYTVILFGSRARGDykiySDYDLLVIgeem---------------pklpPTDAIELhf 83  Sulfolobus toko...
YP_378910      8 DSHLHIIRSIFKQYqa------iNKVLIYGSRAKGNyserSDVDLVICdttfdrktigkillainnsdfpyTVDLQIMen 81  Chlorobium chlo...
YP_746425      9 QAAITRLCHIFSQYpq------iDSVILYGSRAKGNyrpgSDIDLSIQgeqldlttllaienqiddlllpwMVDLSLFhk 82  Nitrosomonas eu...
Feature 1                                     
1KNY_A        83 eilldyasqv--esdwplthgqfFSILPI 109 Staphylococcus aureus
YP_148564     85 ihneq------------lkmnidQEGKTI 101 Geobacillus kaustophilus HTA426
NP_782036     78 ltkkdl----------iknilneGVVIYR 96  Clostridium tetani E88
NP_623562     92 lcrke------------fresilKDGVEI 108 Thermoanaerobacter tengcongensis MB4
YP_920815     90 eelgdplvt---rmltpcrmlynGLGIQE 115 Thermofilum pendens Hrk 5
EDO56104      80 lknadl----------lehihrmGIPIFS 98  Bacteroides uniformis ATCC 8492
YP_001041547  89 sqasd-----------piydemfRTAIKL 106 Staphylothermus marinus F1
NP_377008     84 vkkekledkirefntividafyeGKVICD 112 Sulfolobus tokodaii str. 7
YP_378910     82 iknkn------------lqehikRVGKEF 98  Chlorobium chlorochromatii CaD3
YP_746425     83 idnpd-----------liehiqrIGIPFY 100 Nitrosomonas eutropha C91

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