Source:
Generated By: https://synbiohub.org/public/igem/igem2sbol/1
Created by: Bowman Clark
Date created: 2016-10-13 11:00:00
Date modified: 2016-10-14 06:26:09
his-tagged PPK2b homologue w/ Anderson Promoter J23106
| Types | DnaRegion |
| Roles | CDS Coding |
| Sequences | BBa_K1988017_sequence (Version 1) |
Description
PPK homologs
Overview
Name: Polyphosphate kinase
Function:
There are three PPK subtypes: PPK1, polyphosphate dependent AMP phosphotransferase (PAP), and PPK2, which catalyze the reversible transfer of phosphate groups between nucleoside phosphates and polyphosphates. [1]
PPK1 favors polyphosphate synthesis, using ATP as the preferred phosphate donor [1][2]
PAP favors polyphosphate hydrolysis
PPK2???s affinity for hydrolysis or synthesis varies by species, and PPK2 tends to use either ATP or GTP as the phosphate receiver/donor. [1][2]
In Microlunatus phosphovorus: M. phosphovorus has four PPK homologs (one PPK1 homolog and three PPK2 homologs), which is a fairly large number, as Actinobacteria species typically only have one to three PPK genes. [1]
Location: Unknown, as some Actinobacteria (Corynebacterium glutamicum) *have PPKs localized in the cytoplasm, whereas other Actinobacteria ( Mycobacterium tuberculosis) have PPKs localized along the membrane. [3]
Cofactors and Modifications: There are currently no known cofactors or modifications of the PPK homologs in M. phosphovorus.
Images: The three-dimensional structure of all proteins were predicted using the I-TASSER software [4]. All images shown are the models with the highest confidence, which is quantitatively measured with a C-score that typically falls within the range [-5,2], in which 2 represents the highest level of confidence, and -5 represents the lowest level of confidence.
PPK1 homolog
Name: Polyphosphate kinase 1
Locus tag: MLP_47700
Image
C-score: 0.64
Gene length: 2,145 base pairs
Protein size: 79.9 kDa
Amino acid sequence: MNAPDLAGDL LEPTGTQTVN DGESDGLPDG RFLDRELSWL AFNSRVLDLA KDAQRVPLLE RAKFLAIFAN NLDEFFMVRV AGLKRRIAAG VAVRTVAGLM PREVHETILT RTRELVTEHS RVFEEEIRPE LAAHGIEILH WHELTPDEME RMRVLFAERI FPVLTPLAVD PSHPFPYISG LSINLAVLVK NPSTGVRQFA RVKVPSVLPR FVRLAEGRFV ALEDVIARHL DQLFTGMQVV QHHVFRVTRN EDVEVEEDDA ENLLVALERE LLRRKVGRPP VRLEVEDDID SKMLELLISE LDISEKEVFA LPGPLDLRGL FSLADLDRAE LKYPAFLPST HPHLAEVETA KPADLFAALK QRDVLLHHPY DSFATSVQRF IEQAADDPQV LAIKQTLYRT SGDSPIIDAL IEAAEAGKQV LALVEIKARF DEQANIAWAR RLEQHGCHVV YGLLGLKTHC KLSMVVRDEP DGLRRYAHIG TGNYNPKTAR LYEDMGLLTA NPIITDDIGR LFNHMSGMSQ ETQYRRLLVA PHGIRTGLID RINNEIANHE DGKPAGIKIK VNSLVDETVT DALYRASQAG VPVDLWVRGI CTIRPGVPGL SENIRVRSIL GRFLEHSRLF WFANGGQASV GIGSADLMHR NLDRRVETLA SITNPAHVAE IEGLFDLAFD PGTAAWLLNA DGTWTQRTTD EDGEPLLDMQ AHLISVKSRR RAAK [5]
Function: PPK1 favors polyphosphate synthesis and catalyzes the transfer of phosphate groups from nucleoside triphosphates to polyphosphates. [1]
pH Range The PPK1 homolog in M. phosphovorus has yet to be characterized, and so there is no data for the pH range in which it functions.
Temperature Range The PPK1 homolog in M. phosphovorus has yet to be characterized, and so there is no data for the temperature range in which it functions.
PPK2 homolog A
Name: Polyphosphate kinase 2
Locus tag: MLP_05750
Image
C-score: -0.47
Gene length: 930 base pairs
Protein size: 36.6 kDa
Amino acid sequence: MFARQVDTDP VIIRENFREY LDHLLHDGYT VRHDEHGSDP DLIDPGGDPV ETWREDYPYD ERMEREIYEQ EKYALQIELL KLQYWVQDTG SRIVILFEGR DAAGKGGTIK RFMEHLNPRA ARVVALTKPT ETELGQWYFQ RYITHLPTAG EIVLFDRSWY NRAGVERVMG FCSDRQYEQF LHQAPLFEEM LVDSGFLLTK FWFSVTQSEQ RTRFAIRQID PVRRWKLSPM DLESLDKWDF YGEAKEAMVL RTDTDFAPWT SIKSNDKKRA RINAMRFFLN QFDYDDKDTS VVYSADPLIV QRSIDSIVD [6]
In Microlunatus phosphovorus: PPK2 homolog A is most phylogenetically similar to the PPK2 in Corynebacteria glutamicum.
Function: Due to PPK2 homolog A???s similarity with the PPK2 in Corynebacteria glutamicum, PPK2 homolog A is predicted to synthesize polyphosphate [1].
Location: Due to PPK2 homolog A???s similarity with the PPK2 in Corynebacteria glutamicum, PPK2 homolog A is predicted to be localized in the cytoplasm. [3]
pH Range PPK2 homolog A in M. phosphovorus has yet to be characterized, and so there is no data for the pH range in which it functions.
Temperature Range PPK2 homolog B in M. phosphovorus has yet to be characterized, and so there is no data for the temperature range in which it functions.
PPK2 homolog B
Name: Polyphosphate kinase 2
Locus tag: MLP_50300
Image
C-score: 0.09
Gene length: 837 base pairs
Protein size: 32.6 kDa
Amino acid sequence: MSKKKQKPRK IPNDVYEAEI FRLQSELVKL QEWVRHTGAR VVVIFEGRDA AGKGGTIKRV TEYLSPRVAR VAALPTPTER EKTQWYFQRY IQHLPAAGEI VLFDRSWYNR AGVEKVMGFC TPQQYALFMR QAPLFEQMLI DEGILLRKYW FSVSDSEQLR RFRSRMSDPV RQWKLSPMDL ESINRWEDYS RAKDEMMVHT DIPVSPWFVV ESDIKKHARL NMISHLLSTI PYTDVPGQKV HLPKRLPASE NYQRPPRELS HYVPDHVSQV MGDPEKSS [7]
In Microlunatus phosphovorus: PPK2 homolog B is most phylogenticaly similar to the PPK found in Mycobacterium tuberculosis. [1]
Function: Due to PPK2 homolog B???s similarity with the PPK2 in Mycobacterium tuberculosis, PPK2 homolog A is predicted to hydrolyze polyphosphate. [1]
Location: Due to PPK2 homolog B???s similarity with the PPK2 in Mycobacterium tuberculosis, PPK2 homolog A is predicted to be localized on the membrane. [3]
pH Range PPK2 homolog B in M. phosphovorus has yet to be characterized, and so there is no data for the pH range in which it functions.
Temperature Range PPK2 homolog B in M. phosphovorus has yet to be characterized, and so there is no data for the temperature range in which it functions.
PPK2 homolog C
Name: Polyphosphate kinase 2
Locus tag: MLP_23310
Image
C-score: 0.69
Gene length: 834 base pairs
The NCBI Reference Sequence, and not the GenBank sequence, was used for PPK2 homolog C. This is the only case in which the two sequences vary from one another.
Protein size: 30.8 kDa [8][9]
Amino acid sequence: MSEVLRLPAG PVDLAALDSR ATPGFPGLGK DHVPALMDQL GTSLADRQEC LFANGRSGDS ARNVLVILQG MDTSGKGGII RHAIGLVDPQ GVKITSFKAP TAEERQHPFL WRITNALPGP GMIGIFDRSQ YEDVLIARVN ELATKQVWSR RYALINNWEQ KLADAGTTII KCYLHITPED QLGRLQARLD DPTKHWKYNP GDLDVRAKWS DYQAAYADAL ERCNTDAAPW YVIPAGRKWY RNWAVAALLD EHLRALGLTW PKAGFDVAEE KQRLAAM [8]
In Microlunatus phosphovorus: PPK2 homolog C is relatively similar to both a PPK2 and a PAP; however, PPK2 homolog C is located in a phylogenetic cluster of uncharacterized polyphosphate kinases. PPK2 homolog C is most phylogenetically similar to a PPK from Corynebacterium genitalium in this uncharacterized cluster. [1]
Function: The phylogenetic cluster in which PPK2 homolog C is located contains PPKs with an undetermined function. Still, due to PPK2 homolog C???s similarity to a PAP, as well as a PPK2, PPK2 homolog C could potentially hydrolyze polyphosphates.
pH Range PPK2 homolog C in M. phosphovorus has yet to be characterized, and so there is no data for the pH range in which it functions.
Temperature Range PPK2 homolog C in M. phosphovorus has yet to be characterized, and so there is no data for the temperature range in which it functions.
References
[1] A. Kawakoshi, H. Nakazawa, J. Fukada, M. Sasagawa, Y. Katano, S. Nakamura, A. Hosoyama, H. Sasaki, N. Ichikawa, S. Hanada, Y. Kamagata, K. Nakamura, S. Yamazaki and N. Fujita, "Deciphering the Genome of Polyphosphate Accumulating Actinobacterium Microlunatus phosphovorus", DNA Research, vol. 19, no. 5, pp. 383-394, 2012.
[2] L. Batten, A. Parnell, N. Wells, A. Murch, P. Oyston and P. Roach, "Biochemical and structural characterization of polyphosphate kinase 2 from the intracellular pathogen Francisella tularensis", Bioscience Reports, vol. 36, no. 1, pp. e00294-e00294, 2015.
[3] "BRENDA - Information on EC 2.7.4.1 - polyphosphate kinase", Brenda-enzymes, 2016. [Online]. Available: http://www.brenda-enzymes.org/enzyme.php?ecno=2.7.4.1. [Accessed: 02- Aug- 2016].
[4] Yang, R. Yan, A. Roy, D. Xu, J. Poisson and Y. Zhang, "The I-TASSER Suite: protein structure and function prediction", Nature Methods, vol. 12, no. 1, pp. 7-8, 2014.
[5] "ppk - Polyphosphate kinase - Microlunatus phosphovorus (strain ATCC 700054 / DSM 10555 / JCM 9379 / NBRC 101784 / NCIMB 13414 / VKM Ac-1990 / NM-1) - ppk gene & protein", Uniprot, 2016. [Online]. Available: http://www.uniprot.org/uniprot/F5XF46#sequences. [Accessed: 03- Aug- 2016].
[6] "ppk2 - Polyphosphate kinase 2 - Microlunatus phosphovorus (strain ATCC 700054 / DSM 10555 / JCM 9379 / NBRC 101784 / NCIMB 13414 / VKM Ac-1990 / NM-1) - ppk2 gene & protein", Uniprot, 2016. [Online]. Available: http://www.uniprot.org/uniprot/F5XK93. [Accessed: 28- Jul- 2016].
[7] "ppk2 - Polyphosphate kinase 2 - Microlunatus phosphovorus (strain ATCC 700054 / DSM 10555 / JCM 9379 / NBRC 101784 / NCIMB 13414 / VKM Ac-1990 / NM-1) - ppk2 gene & protein", Uniprot , 2016. [Online]. Available: http://www.uniprot.org/uniprot/F5XH36. [Accessed: 28- Jul- 2016].
[8] "phosphate--nucleotide phosphotransferase [Microlunatus phosphovorus] - Protein - NCBI", National Center for Biotechnology Information, 2016. [Online]. Available: http://www.ncbi.nlm.nih.gov/protein/754172679?report=genpept. [Accessed: 01- Aug- 2016].
[9] "Protein Molecular Weight Calculator", Science Gateway, 2016. [Online]. Available: http://www.sciencegateway.org/tools/proteinmw.htm. [Accessed: 28- Jul- 2016].
Notes
Codon optimized for E. coli K-12 using IDT Codon OptimizerSource
Genetic sequence from 'Deciphering the Genome of Polyphosphate Accumulating Actinobacterium Microlunatus Phosphovorus' by Kawakoshi, et. al.| Access | Instance | Definition |
| public public public public | BBa_J23106 BBa_J34803 BBa_K1988016 BBa_K844000 | BBa_J23106 BBa_J34803 BBa_K1988016 BBa_K844000 |
| Sequence Annotation | Location | Component / Role(s) |
| BBa_J23106 BBa_J34803 BBa_K1988016 BBa_K844000 | 1,35 44,56 63,896 905,940 | BBa_J23106 BBa_J34803 BBa_K1988016 BBa_K844000 |