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Conserved domains on  [gi|17402882|ref|NP_490649|]
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deoxyribonuclease-2-beta isoform 2 [Homo sapiens]

Protein Classification

phospholipase D-like domain-containing protein; phospholipase D family protein( domain architecture ID 10173832)

phospholipase D-like domain-containing protein may hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group, and may also catalyze the transphosphatidylation of phospholipids to acceptor alcohols; phospholipase D family protein similar to Escherichia coli cardiolipin synthase C and Neisseria gonorrhoeae phospholipase D; hydrolyzes phospholipid phosphodiester bonds

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLDc_DNaseII_beta_2 cd09192
Catalytic domain, repeat 2, of Deoxyribonuclease II beta and similar proteins; Catalytic ...
 13-152 1.26e-96

Catalytic domain, repeat 2, of Deoxyribonuclease II beta and similar proteins; Catalytic domain, repeat 2, of Deoxyribonuclease II beta (DNase II beta, EC 3.1.22.1), also known as DNase II-like acid DNase (DLAD), and similar proteins. DNase II is a monomeric nuclease that contains two copies of a variant HKD motif, where the aspartic acid residue is not conserved. The HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily. The catalytic center of DNase II is formed by the two variant HKD motifs from the N- and C-terminal domains in a pseudodimeric way. Members of this family are mainly found in metazoans, and vertebrate proteins have been further classified into DNase II alpha and beta. DNase II beta, or DLAD, is a novel mammalian divalent cation-independent endonuclease with homology to DNase II alpha. It is highly expressed in the eye lens and in salivary glands and is responsible for the degradation of nuclear DNA during lens cell differentiation. DLAD mainly exists as a cytoplasmic protein and cleaves DNA to produce 3'-phosphoryl/5'-hydroxyl ends. Like DNase II alpha, DLAD is active under acidic conditions with maximum activity at pH 5.2. Aurintricarboxylic acid and Zn2+ are effective inhibitors of DLAD activity. Mice deficient in DLAD develop cataracts as they are unable to degrade DNA during differentiation of the lens cells.


:

Pssm-ID: 197288  Cd Length: 139  Bit Score: 274.74  E-value: 1.26e-96
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17402882  13 IPGRLLTTLQSAQGQKFLHFAKSDSFLDDIFAAWMAQRLKTHLLTETWQRKRQELPSNCSLPYHVYNIKAIKLSRHSYFS 92
Cdd:cd09192   1 IPERRLAKLQSAQGEKFLHFAKSKYFVDDIFTAWVAQKLKTDLLVETWQHKGQELPSNCSLPYHVYNINRIGLPGLSTFS 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 17402882  93 SYQDHAKWCISQKGtKNRWTCIGDLNRSPHQAFRSGGFICTQNWQIYQAFQGLVLYYESC 152
Cdd:cd09192  81 SRYDHSKWCVSQKF-KDQWTCIGDLNRSPEQAWRSGGFICTQNKHIYKAFRKLVLYYKSC 139
 
Name Accession Description Interval E-value
PLDc_DNaseII_beta_2 cd09192
Catalytic domain, repeat 2, of Deoxyribonuclease II beta and similar proteins; Catalytic ...
 13-152 1.26e-96

Catalytic domain, repeat 2, of Deoxyribonuclease II beta and similar proteins; Catalytic domain, repeat 2, of Deoxyribonuclease II beta (DNase II beta, EC 3.1.22.1), also known as DNase II-like acid DNase (DLAD), and similar proteins. DNase II is a monomeric nuclease that contains two copies of a variant HKD motif, where the aspartic acid residue is not conserved. The HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily. The catalytic center of DNase II is formed by the two variant HKD motifs from the N- and C-terminal domains in a pseudodimeric way. Members of this family are mainly found in metazoans, and vertebrate proteins have been further classified into DNase II alpha and beta. DNase II beta, or DLAD, is a novel mammalian divalent cation-independent endonuclease with homology to DNase II alpha. It is highly expressed in the eye lens and in salivary glands and is responsible for the degradation of nuclear DNA during lens cell differentiation. DLAD mainly exists as a cytoplasmic protein and cleaves DNA to produce 3'-phosphoryl/5'-hydroxyl ends. Like DNase II alpha, DLAD is active under acidic conditions with maximum activity at pH 5.2. Aurintricarboxylic acid and Zn2+ are effective inhibitors of DLAD activity. Mice deficient in DLAD develop cataracts as they are unable to degrade DNA during differentiation of the lens cells.


Pssm-ID: 197288  Cd Length: 139  Bit Score: 274.74  E-value: 1.26e-96
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17402882  13 IPGRLLTTLQSAQGQKFLHFAKSDSFLDDIFAAWMAQRLKTHLLTETWQRKRQELPSNCSLPYHVYNIKAIKLSRHSYFS 92
Cdd:cd09192   1 IPERRLAKLQSAQGEKFLHFAKSKYFVDDIFTAWVAQKLKTDLLVETWQHKGQELPSNCSLPYHVYNINRIGLPGLSTFS 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 17402882  93 SYQDHAKWCISQKGtKNRWTCIGDLNRSPHQAFRSGGFICTQNWQIYQAFQGLVLYYESC 152
Cdd:cd09192  81 SRYDHSKWCVSQKF-KDQWTCIGDLNRSPEQAWRSGGFICTQNKHIYKAFRKLVLYYKSC 139
DNase_II pfam03265
Deoxyribonuclease II;
1-141 2.80e-63

Deoxyribonuclease II;


Pssm-ID: 460868 [Multi-domain]  Cd Length: 316  Bit Score: 196.34  E-value: 2.80e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17402882     1 MPQLCTRASSSEIPGRLLTTLQSAQGQKFLHFAKSDSFLDDIFAAWMAQRLKTHLLTETWQRKR-QELPSNCSLPYHVYN 79
Cdd:pfam03265 176 LQNLCNGSHTRKSPWDSSVTLTSLDGVTFISFAKSGKFGDDLYSDWVAPTLKSDLLVETWQRGAgGILPSNCSLPYHVYN 255

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17402882    80 IKAIKLSRHSYFSSYQDHAKWCISQKGTKnRWTCIGDLNRSPHQAFRSGGFICTQNWQIYQA 141
Cdd:pfam03265 256 IKQIKIPGSKSFKSTKDHSKWAVSTTSND-PWVCIGDINRQESQEKRGGGTVCIKNPILWKA 316
 
Name Accession Description Interval E-value
PLDc_DNaseII_beta_2 cd09192
Catalytic domain, repeat 2, of Deoxyribonuclease II beta and similar proteins; Catalytic ...
 13-152 1.26e-96

Catalytic domain, repeat 2, of Deoxyribonuclease II beta and similar proteins; Catalytic domain, repeat 2, of Deoxyribonuclease II beta (DNase II beta, EC 3.1.22.1), also known as DNase II-like acid DNase (DLAD), and similar proteins. DNase II is a monomeric nuclease that contains two copies of a variant HKD motif, where the aspartic acid residue is not conserved. The HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily. The catalytic center of DNase II is formed by the two variant HKD motifs from the N- and C-terminal domains in a pseudodimeric way. Members of this family are mainly found in metazoans, and vertebrate proteins have been further classified into DNase II alpha and beta. DNase II beta, or DLAD, is a novel mammalian divalent cation-independent endonuclease with homology to DNase II alpha. It is highly expressed in the eye lens and in salivary glands and is responsible for the degradation of nuclear DNA during lens cell differentiation. DLAD mainly exists as a cytoplasmic protein and cleaves DNA to produce 3'-phosphoryl/5'-hydroxyl ends. Like DNase II alpha, DLAD is active under acidic conditions with maximum activity at pH 5.2. Aurintricarboxylic acid and Zn2+ are effective inhibitors of DLAD activity. Mice deficient in DLAD develop cataracts as they are unable to degrade DNA during differentiation of the lens cells.


Pssm-ID: 197288  Cd Length: 139  Bit Score: 274.74  E-value: 1.26e-96
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17402882  13 IPGRLLTTLQSAQGQKFLHFAKSDSFLDDIFAAWMAQRLKTHLLTETWQRKRQELPSNCSLPYHVYNIKAIKLSRHSYFS 92
Cdd:cd09192   1 IPERRLAKLQSAQGEKFLHFAKSKYFVDDIFTAWVAQKLKTDLLVETWQHKGQELPSNCSLPYHVYNINRIGLPGLSTFS 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 17402882  93 SYQDHAKWCISQKGtKNRWTCIGDLNRSPHQAFRSGGFICTQNWQIYQAFQGLVLYYESC 152
Cdd:cd09192  81 SRYDHSKWCVSQKF-KDQWTCIGDLNRSPEQAWRSGGFICTQNKHIYKAFRKLVLYYKSC 139
DNase_II pfam03265
Deoxyribonuclease II;
1-141 2.80e-63

Deoxyribonuclease II;


Pssm-ID: 460868 [Multi-domain]  Cd Length: 316  Bit Score: 196.34  E-value: 2.80e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17402882     1 MPQLCTRASSSEIPGRLLTTLQSAQGQKFLHFAKSDSFLDDIFAAWMAQRLKTHLLTETWQRKR-QELPSNCSLPYHVYN 79
Cdd:pfam03265 176 LQNLCNGSHTRKSPWDSSVTLTSLDGVTFISFAKSGKFGDDLYSDWVAPTLKSDLLVETWQRGAgGILPSNCSLPYHVYN 255

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17402882    80 IKAIKLSRHSYFSSYQDHAKWCISQKGTKnRWTCIGDLNRSPHQAFRSGGFICTQNWQIYQA 141
Cdd:pfam03265 256 IKQIKIPGSKSFKSTKDHSKWAVSTTSND-PWVCIGDINRQESQEKRGGGTVCIKNPILWKA 316
PLDc_DNaseII_2 cd09121
Catalytic domain, repeat 2, of Deoxyribonuclease II and similar proteins; Catalytic domain, ...
 14-152 3.80e-57

Catalytic domain, repeat 2, of Deoxyribonuclease II and similar proteins; Catalytic domain, repeat 2, of Deoxyribonuclease II (DNase II, EC 3.1.22.1), an endodeoxyribonuclease with ubiquitous tissue distribution. It is essential for accessory apoptotic DNA fragmentation and DNA clearance during development, as well as in tissue regeneration in higher eukaryotes. Unlike the majority of nucleases, DNase II functions optimally at acidic pH in the absence of divalent metal ion cofactors. It hydrolyzes the phosphodiester backbone of DNA by a single strand cleavage mechanism to generate 3'-phosphate termini. The majority of family members contain an N-terminal signal-peptide leader sequence, which is critical for N-glycosylation and DNase II activity. DNase II is a monomeric nuclease that contains two copies of a variant HKD motif, where the aspartic acid residue is not conserved. The HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily. The catalytic center of DNase II is formed by the two variant HKD motifs from the N- and C-terminal domains in a pseudodimeric way. Members of this family are mainly found in metazoans, and vertebrate proteins have been further classified into DNase II alpha and beta (also known as DNase II-like acid DNase, DLAD) subtypes. A few homologs are found in non-metazoan species, but none are found in fungi, plants or prokaryotes, with the sole exception of Burkholderia pseudomallei. Among those homologs, the Caenorhabditis elegans C07B5.5 ORF encoding NUC-1 apoptotic nuclease, the uncharacterized C. elegans crn-6 (cell death related nuclease) gene encoding protein, and the putative gene CG7780 encoding Drosophila DNase II (dDNase II) have similar cleavage activity and specificity to mammalian DNase II enzymes. They may function like an acid DNase implicated in degrading DNA from apoptotic cells engulfed by macrophages. Plancitoxin I, the major lethal factor from the Acanthaster planci venom, is a unique homolog of mammalian DNase II. It has potent hepatotoxicity and the optimum pH for its activity is 7.2, unlike the optimum acidic PH for mammalian DNase II. Some members of this family contain substitutions of conserved residues found in the putative active site, which suggest that these proteins may have diverged from the canonical DNase II activity and may perform other functions.


Pssm-ID: 197220  Cd Length: 139  Bit Score: 174.73  E-value: 3.80e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17402882  14 PGRLLTTLQSAQGQKFLHFAKSDSFLDDIFAAWMAQRLKTHLLTETWQRKRQELPSNCSLPYHVYNIKAIKLSRHSYFSS 93
Cdd:cd09121   2 PWQSSLELKSLGGVSFTSFAKSSKWGKDLYSDLVAPTLKTDLLVETWRGGGGNLPSDCSSKYKVYNVKSISLPGDIAFKS 81

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 17402882  94 YQDHAKWCISQKGTKNrWTCIGDLNRSPHQAFRSGGFICTQNWQIYQAFQGLVLYYESC 152
Cdd:cd09121  82 TKDHSKWAVSVDSSKP-WVCIGDINRQESQFKRGGGTVCFKNKKLWKAFRKSVIDVEPC 139
PLDc_DNaseII_alpha_2 cd09191
Catalytic domain, repeat 2, of Deoxyribonuclease II alpha and similar proteins; Catalytic ...
 20-152 1.05e-41

Catalytic domain, repeat 2, of Deoxyribonuclease II alpha and similar proteins; Catalytic domain, repeat 2, of Deoxyribonuclease II alpha (DNase II alpha, EC 3.1.22.1) and similar proteins. DNase II is a monomeric nuclease that contains two copies of a variant HKD motif, where the aspartic acid residue is not conserved. The HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily. The catalytic center of DNase II is formed by the two variant HKD motifs from the N- and C-terminal domains in a pseudodimeric way. Members of this family are mainly found in metazoans, and vertebrate proteins have been further classified into DNase II alpha and beta. DNase II alpha is an acidic endonuclease found in lysosomes, nuclei, and various secretions. It plays a critical role in the degradation of nuclear DNA expelled from erythroid precursor cells, as well as in the degradation of the apoptotic DNA after macrophages engulf them. It cleaves double-stranded DNA to short 3'-phosphoryl oligonucleotides, rather than 3'-hydroxyl groups, and functions optimally at acidic pH in the absence of divalent metal ion cofactors.


Pssm-ID: 197287  Cd Length: 137  Bit Score: 135.83  E-value: 1.05e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17402882  20 TLQSAQGQKFLHFAKSDSFLDDIFAAWMAQRLKTHLLTETWQRKRQELPSNCSLPYHVYNIKAIKLSRHSYFSSYQDHAK 99
Cdd:cd09191   8 TLTSAGGTNFISFAKGASFGDDLYSGWVAPALQSDLLVQFWVRSTGVLPSNCSLGWKVLDVTRINFPKTSSFKSSQDHSK 87

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 17402882 100 WCISQKGTknrWTCIGDLNRSPHQAFRSGGFICTQNWQIYQAFQGLVLYYESC 152
Cdd:cd09191  88 WCVSTKAG---WVCVGDMNRNMAEEQRGGGTVCLRDPAVWKAFRTLVVDYEDC 137
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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