Pepsin: Difference between revisions
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<StructureSection load='5pep' size=' | <StructureSection load='5pep' size='350' side='right' scene='Sandbox_179/Default/1' caption='Pig pepsin (PDB code [[5pep]])'> | ||
==Introduction== | |||
Theodor Schwann discovered [[Pepsin]] in 1836. He named the enzyme pepsis from the Greek word peptein which means to digest. Pepsin was the first animal enzyme to be discovered, and, in 1929, it became one of the first enzymes to be crystallized, by John H. Northrop. | Theodor Schwann discovered [[Pepsin]] in 1836. He named the enzyme pepsis from the Greek word peptein which means to digest. Pepsin was the first animal enzyme to be discovered, and, in 1929, it became one of the first enzymes to be crystallized, by John H. Northrop. | ||
Pepsin was also the first crystallized protein to be studied by X-ray diffraction using the method of capillary mounting to prevent water loss <ref name="Xray">PMID: 2115088</ref>. | Pepsin was also the first crystallized protein to be studied by X-ray diffraction using the method of capillary mounting to prevent water loss <ref name="Xray">PMID: 2115088</ref>. | ||
*'''Pepsinogen''' is the inactive precursor of pepsin. It is converted to the active pepsin by the hydrochloric acid in the stomach<ref>PMID:8260073</ref>. | |||
*'''Endothiapepsin''' is pepsin from ''Endothia parasitica'' which is used for fragment screening<ref>PMID:27400756</ref>. | |||
See also: | |||
*[[Pepsin (Hebrew)]] | |||
*[[Proteinase]] | |||
==Protein Function== | ==Protein Function== | ||
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One of the main salt bridges in pepsin includes residues from one of the dyad-related hylices (h’N and h’C) and a residue from the opposite lobe, e.g. Asp138 interacts with Arg316. For an image of these residues refer to image 1. bellow. This ion-pair may be important for the stability of the pepsin fold, since chemical modification of Arg316 with butane-2,3-dione partially inactivates the enzyme, as does treatment with phenylglyoxal <ref name="Xray" />. | One of the main salt bridges in pepsin includes residues from one of the dyad-related hylices (h’N and h’C) and a residue from the opposite lobe, e.g. Asp138 interacts with Arg316. For an image of these residues refer to image 1. bellow. This ion-pair may be important for the stability of the pepsin fold, since chemical modification of Arg316 with butane-2,3-dione partially inactivates the enzyme, as does treatment with phenylglyoxal <ref name="Xray" />. | ||
Image 1. The hydrogen bonds between Asp138 and Arg316[[Image:Hydrogen bond.png|450 px ]] | Image 1. The hydrogen bonds between Asp138 and Arg316[[Image:Hydrogen bond.png|450 px ]] | ||
There are many sub domains in pepsin. One sub domain which includes the residues 222-235; 255-276; and 283-290. Portions of this sub domains can interact with inhibitors, and therefore contribute to the structural delineation of S’ sub sites <ref name="flexible" />. It is also possible that ridged movements of sub domains relative to the large domain may help the enzyme adjust to various substrate structures. Furthermore, local regional flexibility of structures such as the “flap,” in and around the active site of pepsin has been suggested to modulate substrate and inhibitor binding <ref name="flexible" />. | There are many sub domains in pepsin. One sub domain which includes the residues 222-235; 255-276; and 283-290. Portions of this sub domains can interact with inhibitors, and therefore contribute to the structural delineation of S’ sub sites <ref name="flexible" />. It is also possible that ridged movements of sub domains relative to the large domain may help the enzyme adjust to various substrate structures. Furthermore, local regional flexibility of structures such as the “flap,” in and around the active site of pepsin has been suggested to modulate substrate and inhibitor binding <ref name="flexible" />. | ||
Once denatured, pepsin is unable to refold to an active native state upon returning from denaturing conditions. One proposed solution for this is that pepsin formation depends on a separate prosegment (PS) domain. When returning from the denatured state, the denatured pepsin first has to bypass a large folding barrier and then in the presence of PS the native state can become thermodynamically stable. The PS therefore can catalyze pepsin folding by stabilizing the transition state <ref name="native" /> . | Once denatured, pepsin is unable to refold to an active native state upon returning from denaturing conditions. One proposed solution for this is that pepsin formation depends on a separate prosegment (PS) domain. When returning from the denatured state, the denatured pepsin first has to bypass a large folding barrier and then in the presence of PS the native state can become thermodynamically stable. The PS therefore can catalyze pepsin folding by stabilizing the transition state <ref name="native" /> . | ||
</StructureSection> | </StructureSection> | ||
==3D structures of pepsin== | ==3D structures of pepsin== | ||
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}} | Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}} | ||
{{#tree:id=OrganizedByTopic|openlevels=0| | |||
*'''Pepsin''' | |||
[[ | **[[1flh]], [[1psn]], [[3utl]] – hPep – human<br /> | ||
[[ | **[[5pep]], [[3pep]], [[4pep]] – pPep – pig<br /> | ||
[[ | **[[1am5]] – Pep – Atlantic cod<br /> | ||
**[[1fmu]], [[1fmx]], [[2jxr]] – yPep – yeast<br /> | |||
[[ | **[[2h6s]], [[2qzw]] – CaPep residues 59-398 – ''Candida albicans''<br /> | ||
**[[1s2b]] – SlPep - ''Scytalidium lignicola''<br /> | |||
[[ | **[[1y43]] – Pep – ''Aspergillus niger''<br /> | ||
**[[1ibq]] - Pep – ''Aspergillus phoenicis''<br /> | |||
[[ | **[[1uh7]], [[1uh8]], [[1uh9]], [[2apr]] – RcPep – ''Rhizopus chinensis''<br /> | ||
[[ | **[[1mpp]] – Pep – ''Rhizomucor pusillus''<br /> | ||
[[ | **[[3app]] – PjPep – ''Penicillium janthinellum''<br /> | ||
[[ | **[[1er8]], [[3er3]], [[4er1]], [[4ape]], [[1ent]] – CpPep – ''Cryphonectria parasitica''<br /> | ||
[[ | **[[3lzy]], [[1oew]] – CpPep residues 90-419 | ||
[[ | |||
[[ | |||
[[ | |||
[[ | |||
[[ | |||
[[ | |||
*Pepsin complex with inhibitor | |||
[[ | **[[1qrp]] – hPep + peptide<br /> | ||
[[ | **[[1pso]] – hPep + pepstatin<br /> | ||
[[ | **[[1yx9]] – pPep + DMSO<br /> | ||
[[ | **[[1psa]], [[1f34]] – pPep + inhibitor<br /> | ||
[[ | **[[6xct]], [[6xcy]], [[6xcz]], [[6xd2]] – pPep + drug<br /> | ||
[[ | **[[1g0v]] – yPep + protease A inhibitor<br /> | ||
[[ | **[[1fq4]], [[1fq5]], [[1fq6]], [[1fq7]], [[1fq8]] - yPep + inhibitor<br /> | ||
[[ | **[[2h6t]] - CaPep residues 59-398 + pepstatin<br /> | ||
[[ | **[[1eag]] - CaPep residues 59-398 + inhibitor<br /> | ||
[[ | **[[2qzx]] - CaPep residues 77-418 + pepstatin<br /> | ||
[[ | **[[1j71]] - Pep + peptide – ''Candida tropicalis''<br /> | ||
**[[2ifr]], [[2ifw]], [[1s2k]] – SlPep + peptide<br /> | |||
**[[1wkr]] - Pep + pepstatin – ''Irpex lacteus''<br /> | |||
**[[4apr]], [[5apr]], [[6apr]] - RcPep + pepstatin<br /> | |||
**[[3apr]] - RcPep + peptide<br /> | |||
**[[2rmp]] - Pep + pepstatin – ''Rhizomucor miehei''<br /> | |||
**[[1nlu]], [[1ga1]], [[1ga4]] - PsPep + pseudo-iodotyrostatin – ''Pseudomonas''<br /> | |||
**[[6m8w]], [[6m8y]] – PsPep + peptide<br /> | |||
**[[6m8f]], [[6m9c]], [[6m9d]], [[1ga6]] - PsPep + statin inhibitor<br /> | |||
**[[1bxo]], [[1bxq]], [[2wea]], [[2web]], [[2wec]], [[2wed]] - PjPep + inhibitor <br /> | |||
**[[1ppk]], [[1apv]], [[1apw]], [[1ppl]], [[1ppm]] – PjPep + peptide analog | |||
**[[1apt]], [[1apu]] – PjPep + pepstatin<br /> | |||
*'''Pepsinogen''' | |||
**[[1avf]] - hPepn<br /> | |||
**[[1yx9]], [[3psg]], [[2psg]] - pPepn<br /> | |||
**[[6row]] – Pepn + cysteine protease + zinc metallopeptidase – worm – Cryo EM<br /> | |||
*'''Endothiapepsin or aspartic proteinase''' | |||
**[[1er8]], [[3er3]], [[4er1]], [[4ape]], [[1ent]], [[5qbk]], [[5qbq]], [[5qbr]], [[5qbs]], [[5qbt]] – CpPep – ''Cryphonectria parasitica''<br /> | |||
**[[5rci]], [[5rcj]], [[5rck]], [[5rcn]], [[5rco]], [[5rcp]], [[5rcr]], [[5rct]], [[5rcu]], [[5rcw]], [[5rcy]], [[5rd0]], [[5rd1]], [[5rd3]], [[5rd5]], [[5rd6]], [[5rd8]], [[5rdb]], [[5rdc]], [[5rdd]], [[5rdf]], [[5rdj]], [[5rdk]], [[5rdl]], [[5rdn]], [[5re3]] – CpETPep ground state<br /> | |||
**[[3lzy]], [[1oew]] – CpPep residues 90-419<br /> | |||
**[[3pb5]], [[3pbd]], [[3pbz]], [[3pcw]], [[3pgi]], [[3pi0]], [[3pld]], [[3pll]], [[3pm4]], [[3pmu]], [[3pmy]] – CpETPep + fragment chemotype<br /> | |||
**[[3pcz]] – CpETPep + benzamidine<br /> | |||
**[[3prs]], [[3pww]] – CpETPep + antiviral drug<br /> | |||
**[[3q6y]], [[1gvx]], [[1gvu]], [[1gvv]], [[1gvw]], [[1gvt]], [[2jji]], [[2jjj]] - CpETPep + pyrrolidine derivative<br /> | |||
**[[5qbj]], [[5qbn]], [[5qbo]], [[5qbp]] - CpETPep + piperidine derivative<br /> | |||
**[[5qbh]], [[5qbi]], [[5qbm]] - CpETPep + pyridine derivative<br /> | |||
**[[5qbl]] - CpETPep + morpholine derivative<br /> | |||
**[[3t6i]], [[5qbg]] - CpETPep + azepine derivative<br /> | |||
**[[3t7p]], [[4lhh]], [[4lbt]], [[4kup]], [[5hco]], [[5hct]], [[5og7]] - CpETPep + hydrazine derivative<br /> | |||
**[[4l6b]], [[3t7x]], [[3t7q]], [[3psy]], [[4lap]] – CpETPwo + thiophen inhibitor<br /> | |||
**[[3er5]], [[4er4]], [[5er2]], [[2er0]], [[2er6]], [[2er7]], [[2er9]], [[5er1]], [[1epl]], [[1epm]], [[1epn]], [[1epo]], [[1epp]], [[1epq]], [[1epr]], [[3uri]], [[3url]] – CpETPep + peptide<br /> | |||
**[[4er2]] - CpETPep + pepstatin<br /> | |||
**[[2v00]], [[1od1]], [[1oex]], [[1eed]], [[1e81]], [[1e82]], [[1e80]], [[1e5o]], [[3wz6]], [[3wz7]], [[3wz8]], [[4y35]], [[4y36]], [[4y37]], [[4y38]], [[4y39]], [[4y3a]], [[4y3d]], [[4y3e]], [[4y3f]], [[4y3g]], [[4y3h]], [[4y3j]], [[4y3l]], [[4y3m]], [[4y3n]], [[4y3p]], [[4y3q]], [[4y3r]], [[4y3s]], [[4y3t]], [[4y3w]], [[4y3x]], [[4y3y]], [[4y3z]], [[4y41]], [[4y43]], [[4y44]], [[4y45]], [[4y47]], [[4y48]], [[4y4a]], [[4y4b]], [[4y4d]], [[4y4e]], [[4y4g]], [[4y4j]], [[4y4t]], [[4y4u]], [[4y4w]], [[4y4x]], [[4y4z]], [[4y50]], [[4y51]], [[4y53]], [[4y54]], [[4y56]], [[4y57]], [[4y58]], [[4y5a]], [[4y5b]], [[4y5c]], [[4y5e]], [[4y5g]], [[4y5k]], [[4y5l]], [[4y5m]], [[4y5n]], [[4y5p]], [[4yck]], [[4yct]], [[4ycy]], [[4yd3]], [[4yd4]], [[4yd5]], [[4yd6]], [[4yd7]], [[4ze6]], [[4zea]], [[5dpz]], [[5dq1]], [[5dq2]], [[5dq4]], [[5dq5]], [[5dr0]], [[5dr1]], [[5dr3]], [[5dr4]], [[5dr7]], [[5dr8]], [[5is4]], [[5isj]], [[5isk]], [[5j25]], [[5lwr]], [[5lws]], [[5lwt]], [[5lwu]], [[5mb0]], [[5mb3]], [[5mb5]], [[5mb6]], [[5mb7]], [[5oje]], [[5oyq]], [[5oyr]], [[5oys]], [[5oyt]], [[5oyu]], [[5oyv]], [[5oyw]], [[5oyx]], [[5oyy]], [[5oyz]], [[5oz0]], [[5oz1]], [[5oz2]], [[5oz3]], [[5oz4]], [[5oz5]], [[5oz6]], [[5oz7]], [[5oz8]], [[5oz9]], [[5oza]], [[5ozb]], [[5ozc]], [[5ozd]], [[5oze]], [[5ozf]], [[5ozg]], [[5ozh]], [[5ozi]], [[5ozj]], [[5ozk]], [[5ozl]], [[5ozm]], [[5ozn]], [[5ozo]], [[5ozp]], [[5ozq]], [[5ozr]], [[5ozs]], [[5ozt]], [[5ozu]], [[5ozv]], [[5ozw]], [[5ozx]], [[5ozy]], [[5ozz]], [[5p00]], [[5p01]], [[5p02]], [[5p03]], [[5p04]], [[5p05]], [[5p06]], [[5p07]], [[5p08]], [[5p09]], [[5p0a]], [[5p0b]], [[5p0c]], [[5p0d]], [[5p0e]], [[5p0f]], [[5p0g]], [[5p0h]], [[5p0i]], [[5p0j]], [[5p0k]], [[5p0l]], [[5p0m]], [[5p0n]], [[5p0o]], [[5p0p]], [[5p0q]], [[5p0r]], [[5p0s]], [[5p0t]], [[5p0u]], [[5p0v]], [[5p0w]], [[5p0x]], [[5p0y]], [[5p0z]], [[5p10]], [[5p11]], [[5p12]], [[5p13]], [[5p14]], [[5p15]], [[5p16]], [[5p17]], [[5p18]], [[5p19]], [[5p1a]], [[5p1b]], [[5p1c]], [[5p1d]], [[5p1e]], [[5p1f]], [[5p1g]], [[5p1h]], [[5p1i]], [[5p1j]], [[5p1k]], [[5p1l]], [[5p1m]], [[5p1n]], [[5p1o]], [[5p1p]], [[5p1q]], [[5p1r]], [[5p1s]], [[5p1t]], [[5p1u]], [[5p1v]], [[5p1w]], [[5p1x]], [[5p1y]], [[5p1z]], [[5p20]], [[5p22]], [[5p23]], [[5p24]], [[5p25]], [[5p26]], [[5p27]], [[5p28]], [[5p29]], [[5p2a]], [[5p2b]], [[5p2c]], [[5p2d]], [[5p2e]], [[5p2f]], [[5p2g]], [[5p2h]], [[5p2i]], [[5p2j]], [[5p2k]], [[5p2l]], [[5p2m]], [[5p2n]], [[5p2o]], [[5p2q]], [[5p2r]], [[5p2s]], [[5p2t]], [[5p2u]], [[5p2v]], [[5p2w]], [[5p2x]], [[5p2y]], [[5p2z]], [[5p30]], [[5p31]], [[5p32]], [[5p33]], [[5p34]], [[5p35]], [[5p36]], [[5p37]], [[5p38]], [[5p39]], [[5p3a]], [[5p3b]], [[5p3c]], [[5p3d]], [[5p3e]], [[5p3f]], [[5p3g]], [[5p3h]], [[5p3i]], [[5p3j]], [[5p3k]], [[5p3l]], [[5p3m]], [[5p3n]], [[5p3o]], [[5p3p]], [[5p3q]], [[5p3r]], [[5p3s]], [[5p3t]], [[5p3u]], [[5p3v]], [[5p3w]], [[5p3x]], [[5p3y]], [[5p3z]], [[5p40]], [[5p41]], [[5p42]], [[5p43]], [[5p44]], [[5p45]], [[5p46]], [[5p47]], [[5p48]], [[5p49]], [[5p4a]], [[5p4b]], [[5p4c]], [[5p4d]], [[5p4e]], [[5p4f]], [[5p4g]], [[5p4h]], [[5p4i]], [[5p4j]], [[5p4k]], [[5p4l]], [[5p4m]], [[5p4n]], [[5p4o]], [[5p4p]], [[5p4q]], [[5p4r]], [[5p4s]], [[5p4t]], [[5p4u]], [[5p4v]], [[5p4w]], [[5p4x]], [[5p4y]], [[5p4z]], [[5p50]], [[5p51]], [[5p52]], [[5p53]], [[5p54]], [[5p55]], [[5p56]], [[5p57]], [[5p58]], [[5p59]], [[5p5a]], [[5p5b]], [[5p5c]], [[5p5d]], [[5p5e]], [[5p5f]], [[5p5g]], [[5p5h]], [[5p5i]], [[5p5j]], [[5p5k]], [[5p5l]], [[5p5m]], [[5p5n]], [[5p5o]], [[5p5p]], [[5p5q]], [[5p5r]], [[5p5s]], [[5p5t]], [[5p5u]], [[5p5v]], [[5p5w]], [[5p5x]], [[5p5y]], [[5p5z]], [[5p60]], [[5p61]], [[5p62]], [[5p63]], [[5p64]], [[5p65]], [[5p66]], [[5p67]], [[5p68]], [[5p69]], [[5p6a]], [[5p6b]], [[5p6c]], [[5p6d]], [[5p6e]], [[5p6f]], [[5p6g]], [[5p6h]], [[5p6i]], [[5p6j]], [[5p6k]], [[5p6l]], [[5p6m]], [[5p6n]], [[5p6o]], [[5p6p]], [[5p6q]], [[5p6r]], [[5p6s]], [[5p6t]], [[5p6u]], [[5p6v]], [[5p6w]], [[5p6x]], [[5p6y]], [[5p6z]], [[5p70]], [[5p71]], [[5p72]], [[5p73]], [[5p74]], [[5p75]], [[5p76]], [[5p77]], [[5p78]], [[5p79]], [[5p7a]], [[5p7b]], [[5p7c]], [[5p7d]], [[5p7e]], [[5p7f]], [[5p7g]], [[5p7h]], [[5p7i]], [[5p7j]], [[5p7k]], [[5p7l]], [[5p7m]], [[5p7n]], [[5p7o]], [[5p7p]], [[5p7q]], [[5p7r]], [[5p7s]], [[5p7t]], [[5p7u]], [[5p7v]], [[5p7w]], [[5p7x]], [[5p7y]], [[5p7z]], [[5p80]], [[5p81]], [[5p82]], [[5p83]], [[5p84]], [[5p85]], [[5p86]], [[5p87]]. [[5p88]], [[5p89]], [[5p8a]]. [[5p8b]], [[5p8c]], [[5p8d]]. [[5p8e]], [[5p8f]], [[5p8g]]. [[5p8h]], [[5p8i]], [[5p8j]]. [[5p8k]], [[5p8l]], [[5p8m]], [[5p8n]], [[5p8o]], [[5p8p]]. [[5p8q]], [[5p8r]], [[5p8s]]. [[5p8t]], [[5p8u]], [[5p8v]], [[5qb5]], [[5qb6]], [[5qb7]], [[5qb8]], [[5qb9]], [[5qba]], [[5qbb]], [[5qbc]], [[5qbd]], [[5qbe]], [[5qbf]], [[5r1t]], [[5r1u]], [[5r1v]], [[5r1w]], [[5r1x]], [[5r1y]], [[5r1z]], [[5r20]], [[5r21]], [[5r22]], [[5r23]], [[5r24]], [[5r25]], [[5r26]], [[5r27]], [[5r28]], [[5r29]], [[5r2a]], [[5r2b]], [[5r2c]], [[5r2d]], [[5r2e]], [[5r2f]], [[5r2g]], [[5r2h]], [[5r2i]], [[5r2j]], [[5r2k]], [[5r2l]], [[5r2m]], [[5r2n]], [[5r2o]], [[5r2p]], [[5r2q]], [[5r2r]], [[5r2s]], [[5r2t]], [[5r2u]], [[5r2v]], [[5r2w]], [[5r2x]], [[5r2y]], [[5r2z]], [[5r30]], [[5r31]], [[5r32]], [[5r33]], [[5r34]], [[5r35]], [[5r36]], [[5r37]], [[5r38]], [[5r39]], [[5r3a]], [[5r3b]], [[5r3c]], [[5r3d]], [[5r3e]], [[5r3f]], [[5r3g]], [[5r3h]], [[5r3i]], [[5r3j]], [[5r3k]], [[5r3l]], [[5r3m]], [[5r3n]], [[5r3o]], [[5r3p]], [[5r3q]], [[5r3r]], [[5r3s]], [[5r3t]], [[5r3u]], [[5r3v]], [[5r3w]], [[5r3x]], [[5r3y]], [[5r3z]], [[5r40]], [[5r41]], [[5rbo]], [[5rbp]], [[5rbq]], [[5rbr]], [[5rbs]], [[5rbt]], [[5rbu]], [[5rbv]], [[5rbw]], [[5rbx]], [[5rby]], [[5rbz]], [[5rcl]], [[5rcm]], [[5rc4]], [[5rc3]], [[5rc2]], [[5rc5]], [[5rc6]], [[5rc7]], [[5rc0]], [[5rc1]], [[5rca]], [[5rcb]], [[5rcc]], [[5rcd]], [[5rch]], [[5rcl]], [[5rcm]], [[5rcq]], [[5rcs]], [[5rce]], [[5rcf]], [[5rcg]], [[5rcx]], [[5rcy]], [[5rcz]], [[5rd2]], [[5rd4]], [[5rd7]], [[5rd9]], [[5rda]], [[5rde]], [[5rdg]], [[5rdh]], [[5rdi]], [[5rdm]], [[5rdo]], [[5rdp]], [[5rdq]], [[5rdr]], [[5rds]], [[5rdt]], [[5rdu]], [[5rdv]], [[5rdw]], [[5rdx]], [[5rdy]], [[5rdz]], [[5re0]], [[5re1]], [[5re2]], [[5sak]], [[5sam]], [[5san]], [[5sao]], [[5sap]], [[5saq]], [[5sas]], [[5sat]], [[6ron]], [[6rsv]], [[6scv]], [[6zz2]], [[7adg]] – CpETPep + inhibitor<br /> | |||
**[[2vs2]], [[1gkt]] - CpETPep + inhibitor - neutron<br /> | |||
**[[3urj]] - ETPep – ''Endothia parasitica''<br /> | |||
}} | |||
=References= | =References= | ||
<references/> | <references/> | ||
[[he:Pepsin_%28Hebrew%29]] | [[he:Pepsin_%28Hebrew%29]] | ||
[[Category:Topic Page]] | [[Category:Topic Page]] |