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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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''' | |||
[[2h6s]], [[2qzw]] – CaPep residues 59-398 – ''Candida albicans''<br /> | **[[1flh]], [[1psn]], [[3utl]] – hPep – human<br /> | ||
[[1s2b]] – SlPep - ''Scytalidium lignicola''<br /> | **[[5pep]], [[3pep]], [[4pep]] – pPep – pig<br /> | ||
[[1y43]] – Pep – ''Aspergillus niger''<br /> | **[[1am5]] – Pep – Atlantic cod<br /> | ||
[[1ibq]] - Pep – ''Aspergillus phoenicis''<br /> | **[[1fmu]], [[1fmx]], [[2jxr]] – yPep – yeast<br /> | ||
**[[2h6s]], [[2qzw]] – CaPep residues 59-398 – ''Candida albicans''<br /> | |||
[[1uh7]], [[1uh8]], [[1uh9]], [[2apr]] – RcPep – ''Rhizopus chinensis''<br /> | **[[1s2b]] – SlPep - ''Scytalidium lignicola''<br /> | ||
[[1mpp]] – Pep – ''Rhizomucor pusillus''<br /> | **[[1y43]] – Pep – ''Aspergillus niger''<br /> | ||
**[[1ibq]] - Pep – ''Aspergillus phoenicis''<br /> | |||
**[[1uh7]], [[1uh8]], [[1uh9]], [[2apr]] – RcPep – ''Rhizopus chinensis''<br /> | |||
[[3app]] – PjPep – ''Penicillium janthinellum''<br /> | **[[1mpp]] – Pep – ''Rhizomucor pusillus''<br /> | ||
**[[3app]] – PjPep – ''Penicillium janthinellum''<br /> | |||
[[1er8]], [[3er3]], [[4er1]], [[4ape]], [[1ent]] – CpPep – ''Cryphonectria parasitica''<br /> | **[[1er8]], [[3er3]], [[4er1]], [[4ape]], [[1ent]] – CpPep – ''Cryphonectria parasitica''<br /> | ||
[[3lzy]], [[1oew]] – CpPep residues 90-419 | **[[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 /> | |||
[[1yx9 | |||
[[ | |||
*'''Endothiapepsin or aspartic proteinase''' | |||
[[1er8]], [[3er3]], [[4er1]], [[4ape]], [[1ent]] – CpPep – ''Cryphonectria parasitica''<br /> | **[[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/> |