| Literature DB >> 23304454 |
Vinod Kumar1, Gopal Singh, A K Verma, Sanjeev Agrawal.
Abstract
Histidine acid phytases (HAPhy) are widely distributed enzymes among bacteria, fungi, plants, and some animal tissues. They have a significant role as an animal feed enzyme and in the solubilization of insoluble phosphates and minerals present in the form of phytic acid complex. A set of 50 reference protein sequences representing HAPhy were retrieved from NCBI protein database and characterized for various biochemical properties, multiple sequence alignment (MSA), homology search, phylogenetic analysis, motifs, and superfamily search. MSA using MEGA5 revealed the presence of conserved sequences at N-terminal "RHGXRXP" and C-terminal "HD." Phylogenetic tree analysis indicates the presence of three clusters representing different HAPhy, that is, PhyA, PhyB, and AppA. Analysis of 10 commonly distributed motifs in the sequences indicates the presence of signature sequence for each class. Motif 1 "SPFCDLFTHEEWIQYDYLQSLGKYYGYGAGNPLGPAQGIGF" was present in 38 protein sequences representing clusters 1 (PhyA) and 2 (PhyB). Cluster 3 (AppA) contains motif 9 "KKGCPQSGQVAIIADVDERTRKTGEAFAAGLAPDCAITVHTQADTSSPDP" as a signature sequence. All sequences belong to histidine acid phosphatase family as resulted from superfamily search. No conserved sequence representing 3- or 6-phytase could be identified using multiple sequence alignment. This in silico analysis might contribute in the classification and future genetic engineering of this most diverse class of phytase.Entities:
Year: 2012 PMID: 23304454 PMCID: PMC3523131 DOI: 10.1155/2012/845465
Source DB: PubMed Journal: Enzyme Res ISSN: 2090-0414
List of retrieved protein sequences from NCBI/Entrez and their accession number.
| S. no. | Source organism | Accession number | Total sequences |
|---|---|---|---|
| 1 |
| P07102.2, NP_415500.1, ZP_07105303.1, YP_001462212.1 | 4 |
| 2 |
| YP_408643.1 | 1 |
| 3 |
| YP_688514.1 | 1 |
| 4 |
| ZP_07681338.1, YP_402619.1 | 2 |
| 5 |
| ZP_02904404.1 | 1 |
| 6 |
| YP_002384142.1 | 1 |
| 9 |
| AAR89622.1 | 1 |
| 10 |
| P34752.1, XP_001401713.2, P34754.1, XP_001393206.1 | 4 |
| 11 |
| XP_001821210.1 | 1 |
| 12 |
| P34753.1 | 1 |
| 13 |
| XP_002376973.1 | 1 |
| 14 |
| XP_751964.2 | 1 |
| 15 |
| XP_001214511.1 | 1 |
| 16 |
| XP_001267160.1 | 1 |
| 17 |
| XP_659289.1 | 1 |
| 18 |
| XP_001271757.1, XP_001271709.1 | 2 |
| 19 |
| XP_002561094.1 | 1 |
| 20 |
| XP_002148821.1 | 1 |
| 21 |
| XP_002629272.1 | 1 |
| 22 |
| XP_001554147.1 | 1 |
| 23 |
| XP_002542954.1 | 1 |
| 24 |
| XP_001538598.1 | 1 |
| 25 |
| XP_001589324.1 | 1 |
| 26 |
| XP_003065081.1 | 1 |
| 27 |
| XP_003233631.1 | 1 |
| 28 |
| XP_002849736.1 | 1 |
| 29 |
| XP_002483691.1 | 1 |
| 30 |
| XP_001906589.1 | 1 |
| 31 |
| XP_003021635.1 | 1 |
| 32 |
| XP_003169494.1 | 1 |
| 33 |
| XP_002150501.1 | 1 |
| 34 |
| XP_003015622.1 | 1 |
| 35 |
| XP_713416.1 | 1 |
| 36 |
| XP_002421792.1, XP_002419861.1 | 2 |
| 37 |
| XP_713478.1 | 1 |
| 38 |
| XP_002546108.1 | 1 |
| 39 |
| XP_458051.2 | 1 |
| 40 |
| XP_002490985.1 | 1 |
| 41 |
| NP_009650.1 | 1 |
| 42 |
| XP_003072016.1 | 1 |
Figure 1Phylogenetic tree constructed by NJ method based on HAPhy protein sequences.
Biochemical characteristics of HAPhy protein sequences.
| S. no. | Accession number | Source organisms | Number of amino acids | Molecular weight | Theoretical pI | Total number of negatively charged residues (Asp + Glu) | Total number of positively charged residues (Arg + Lys) | Instability index | Aliphatic index | GRAVY | Predictive active sites by Pfam |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | P07102.2 |
| 523 | 56118.9 | 6.07 | 51 | 43 | 45.95 | 86.25 | −0.221 | 39(H), 326(D) |
| 2 | NP_415500.1 |
| 432 | 47056.8 | 6.26 | 40 | 37 | 38.08 | 93.08 | −0.157 | 39(H), 326(D) |
| 3 | ZP_07105303.1 |
| 442 | 48081 | 6.09 | 41 | 37 | 39.71 | 92.08 | −0.147 | 49(H), 336(D) |
| 4 | YP_001462212.1 |
| 432 | 47029.8 | 6.09 | 40 | 36 | 38.56 | 93.31 | −0.138 | 39(H), 326(D) |
| 5 | ZP_07141224.1 |
| 442 | 48081 | 6.26 | 41 | 38 | 39.52 | 92.08 | −0.148 | 49(H), 336(D) |
| 6 | YP_408643.1 |
| 432 | 47063.8 | 6.09 | 40 | 36 | 37.99 | 92.41 | −0.141 | 39(H), 326(D) |
| 7 | YP_688514.1 |
| 432 | 47105.9 | 5.94 | 40 | 35 | 38.2 | 92.87 | −0.131 | 39(H), 326(D) |
| 8 | ZP_07681338.1 |
| 434 | 47354.1 | 5.55 | 42 | 34 | 38.57 | 93.99 | −0.142 | 41(H), 328(D) |
| 9 | YP_402619.1 |
| 434 | 47328 | 5.55 | 42 | 34 | 38.57 | 93.09 | −0.152 | 41(H), 328(D) |
| 10 | ZP_02904404.1 |
| 439 | 48000.6 | 9.35 | 33 | 44 | 37.78 | 96.88 | −0.094 | 46(H), 333(D) |
| 11 | YP_002384142.1 |
| 428 | 46608.5 | 8.37 | 32 | 35 | 40.79 | 93.48 | −0.132 | 39(H), 322(D) |
| 12 | AAR89622.1 |
| 433 | 48506.5 | 6.29 | 49 | 47 | 35.09 | 86 | −0.322 | 39(H), 325(D) |
| 13 | P34752.1 |
| 467 | 51086 | 4.94 | 51 | 34 | 44.72 | 76.62 | −0.211 | 82(H), 382(D) |
| 14 | P34753.1 |
| 467 | 51074.9 | 4.89 | 52 | 33 | 42.73 | 76.85 | −0.221 | 82(H), 382(D) |
| 15 | XP_001401713.2 |
| 497 | 54579.1 | 5.25 | 53 | 38 | 44.74 | 77.69 | −0.225 | 112(H), 392(D) |
| 16 | XP_001821210.1 |
| 466 | 51257.1 | 4.87 | 57 | 39 | 34.89 | 70.49 | −0.316 | 81(H), 361(D) |
| 17 | XP_002376973.1 |
| 496 | 54729.2 | 5.11 | 60 | 46 | 35.72 | 72.7 | −0.31 | 111(H), 391(D) |
| 18 | XP_751964.2 |
| 498 | 54538.8 | 8.53 | 48 | 53 | 29.31 | 77.59 | −0.197 | 114(H), 393(D) |
| 19 | XP_001214511.1 |
| 466 | 51088.1 | 5.12 | 51 | 33 | 35.3 | 72.94 | −0.226 | 82(H), 382(D) |
| 20 | XP_001267160.1 |
| 464 | 50787.1 | 6.17 | 47 | 43 | 31.33 | 73.17 | −0.206 | 80(H), 359(D) |
| 21 | XP_659289.1 |
| 463 | 51816.2 | 5.35 | 52 | 39 | 32.09 | 72.48 | −0.287 | 80(H), 358(D) |
| 22 | XP_001271757.1 |
| 465 | 51531.3 | 7.14 | 52 | 52 | 29.94 | 72.6 | −0.332 | 81(H), 360(D) |
| 23 | XP_002561094.1 |
| 483 | 53668.6 | 7.11 | 51 | 51 | 46.27 | 69.65 | −0.393 | 96(H), 378(D) |
| 24 | XP_002148821.1 |
| 465 | 50878 | 5.19 | 48 | 37 | 32.37 | 73.46 | −0.172 | 80(H), 360(D) |
| 25 | XP_002629272.1 |
| 528 | 58565.2 | 6.21 | 55 | 49 | 44 | 80.49 | −0.167 | 140(H), 420(D) |
| 26 | XP_001554147.1 |
| 529 | 57902.2 | 5.08 | 55 | 42 | 40.6 | 69.38 | −0.329 | 140(H), 423(D) |
| 27 | XP_002542954.1 |
| 501 | 56117.4 | 8.51 | 52 | 57 | 33.68 | 70.08 | −0.448 | 108(H), 388(D) |
| 28 | XP_001538598.1 |
| 441 | 49342.6 | 5.88 | 46 | 35 | 44.48 | 79.59 | −0.238 | 53(H), 333(D) |
| 29 | XP_001589324.1 |
| 465 | 50709.3 | 4.88 | 45 | 29 | 38.75 | 73.25 | −0.188 | 76(H), 359(D) |
| 30 | XP_003065081.1 |
| 539 | 60239.3 | 7.93 | 61 | 63 | 29.66 | 75.25 | −0.368 | 145(H), 425(D) |
| 31 | XP_003233631.1 |
| 474 | 52142.7 | 6.23 | 54 | 50 | 41.86 | 69.22 | −0.331 | 87(H), 362(D) |
| 32 | XP_002849736.1 |
| 466 | 51429.8 | 5.58 | 53 | 45 | 40.37 | 67.04 | −0.33 | 85(H), 360(D) |
| 33 | XP_002483691.1 |
| 523 | 58182.2 | 4.9 | 65 | 42 | 42.55 | 78.7 | −0.26 | 129(H), 409(D) |
| 34 | XP_001906589.1 |
| 514 | 57367.6 | 5.55 | 63 | 53 | 36.91 | 77.8 | −0.396 | 125(H), 406(D) |
| 35 | XP_003021635.1 |
| 456 | 50332.6 | 6.27 | 53 | 49 | 41.1 | 66.36 | −0.372 | 69(H), 344(D) |
| 36 | XP_003169494.1 |
| 473 | 52338.9 | 6.33 | 54 | 51 | 38.25 | 67.06 | −0.353 | 86(H), 361(D) |
| 37 | XP_002150501.1 |
| 510 | 57067.8 | 5.07 | 64 | 45 | 40.04 | 74.18 | −0.345 | 116(H), 396(D) |
| 38 | XP_003015622.1 |
| 456 | 50490.7 | 6.14 | 54 | 49 | 43.2 | 65.72 | −0.4 | 69(H), 344(D) |
| 39 | P34754.1 |
| 479 | 52611.5 | 4.65 | 48 | 28 | 34.04 | 71.96 | −0.279 | 82(H), 382(D) |
| 40 | XP_001393206.1 |
| 479 | 52486.2 | 4.62 | 49 | 27 | 33.71 | 71.17 | −0.289 | 82(H), 382(D) |
| 41 | XP_001271709.1 |
| 460 | 50746.9 | 4.61 | 54 | 31 | 39.64 | 79.96 | −0.17 | 69(H), 329(D) |
| 42 | XP_713416.1 |
| 461 | 51283.1 | 5.8 | 48 | 43 | 29.87 | 74.27 | −0.44 | 73(H), 335(D) |
| 43 | XP_002421792.1 |
| 462 | 51275.9 | 5.44 | 48 | 41 | 28.02 | 72.62 | −0.411 | 73(H), 335(D) |
| 44 | XP_713478.1 |
| 462 | 51305 | 5.57 | 48 | 42 | 27.7 | 71.99 | −0.426 | 73(H), 335(D) |
| 45 | XP_002546108.1 |
| 465 | 52540.6 | 4.41 | 67 | 35 | 33.65 | 67.74 | −0.543 | 73(H), 337(D) |
| 46 | XP_458051.2 |
| 464 | 51835.7 | 5.13 | 52 | 37 | 39.65 | 73.1 | −0.404 | 73(H), 337(D) |
| 47 | XP_002419861.1 |
| 457 | 52259.6 | 5.2 | 57 | 46 | 36.41 | 70.55 | −0.493 | 73(H), 332(D) |
| 48 | XP_002490985.1 |
| 468 | 52690.7 | 4.41 | 68 | 33 | 37.25 | 84.19 | −0.27 | 84(H), 346(D) |
| 49 | NP_009650.1 |
| 467 | 52776.5 | 4.43 | 67 | 36 | 30.82 | 71.46 | −0.373 | 75(H), 338(D) |
| 50 | XP_003072016.1 |
| 403 | 45575.2 | 5.82 | 51 | 42 | 31.24 | 70.97 | −0.473 | 4(H), 269(D) |
Distribution of superfamily among HAPhy protein sequences determined using superfam server.
| Family | Superfamily | Accession number (range of amino acids residues) |
|---|---|---|
| Histidine acid phosphatase | Phosphoglycerate mutase-like | XP_001401713.2 (61–496), P07102.2 (26–429), NP_415500.1 (26–429), ZP_07105303.1 (36–439), YP_001462212.1 (26–429), ZP_07141224.1 (36–439), YP_408643.1 (26–429), YP_688514.1 (26–429), ZP_07681338.1 (28–431), YP_402619.1 (28–431), ZP_02904404.1 (33–436) YP_002384142.1 (27–424), AAR89622.1 (27–427), P34752.1 (30–466), P34753.1 (31–466), XP_001821210.1 (29–465), XP_002376973.1 (59–495), XP_751964.2 (62–497), XP_001214511.1 (32–466), XP_001267160.1 (28–463), XP_659289.1 (28–461), XP_001271757.1 (30–464), XP_002561094.1 (45–482), XP_002148821.1 (28–464), XP_002629272.1 (89–527), XP_001554147.1 (90–527), XP_002542954.1 (57–495), XP_001538598.1 (6–440), XP_001589324.1 (26–463), XP_003065081.1 (97–532), XP_003233631.1 (36–469), XP_002849736.1 (35–466), XP_002483691.1 (87–517), XP_001906589.1 (76–512), XP_003021635.1 (23–451), XP_003169494.1 (35–468), XP_002150501.1 (73–505), XP_003015622.1 (23–451), P34754.1 (35–470), XP_001393206.1 (35–470), XP_001271709.1 (23–452), XP_713416.1 (28–455), XP_002421792.1 (28–455), XP_713478.1 (28–455), XP_002546108.1 (28–457), XP_458051.2 (28–451), XP_002419861.1 (28–445), XP_002490985.1 (42–464), NP_009650.1 (34–460), XP_003072016.1 (1–393) |
Distribution of commonly observed motifs in different HAPhy protein sequences along with their functional domains.
| Motifs number | Motif present in number of sequence | Motif width | Sequence | Domain |
|---|---|---|---|---|
| 1 | 38 | 41 | SPFCDLFTHEEWIQYDYLQSLGKYYGYGAGNPLGPAQGIGF | HP_HAP_like, histidine phosphatases superfamily |
| 2 | 49 | 29 | VPPGCKITFVQVLSRHGARYPTKSKSKMY | Histidine phosphatase superfamily |
| 3 | 47 | 30 | VRVLVNDRVVPLHGCLVDPLGRCKLDDFVA | Local conserved domain |
| 4 | 49 | 29 | TLYADFSHDNDMTSIFTALGLYNGTEPLS | Histidine phosphatase superfamily |
| 5 | 26 | 50 | YAFLKTYNYSLGADDLTPFGEQQLVDSGIKFYQRYESLAKDIVPFIRASG | Histidine phosphatase superfamily |
| 6 | 49 | 29 | RLNKALPGVNLTSADVVSLMDMCSFETVA | Histidine phosphatase superfamily |
| 7 | 48 | 21 | GYSAAWTVPFGARAYFEKMQC | Histidine phosphatase superfamily |
| 8 | 11 | 50 | TEIFLLQQAQGMPEPGWGRITDSHQWNTLLSLHNAQFYLLQRTPEVARSR | Local conserved domain |
| 9 | 12 | 50 | KKGCPQSGQVAIIADVDERTRKTGEAFAAGLAPDCAITVHTQADTSSPDP | Histidine phosphatase superfamily |
| 10 | 9 | 50 | TPHPPQKQAYGVTLPTSVLFIAGHDTNLANLGGALELNWTLPGQPDNTPP | Histidine phosphatase superfamily |