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2w5m

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Revision as of 05:01, 19 November 2020

RNASE A-PYROPHOSPHATE ION COMPLEX

Structural highlights

2w5m is a 2 chain structure with sequence from Bos taurus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	1ssb, 1afu, 1w4q, 1c0b, 6rat, 1ymr, 1o0o, 8rsa, 5rsa, 1rno, 7rat, 2w5l, 1izq, 1eid, 1cjq, 1eos, 1rnn, 1j82, 1qhc, 1ymw, 1o0h, 1afk, 1f0v, 1dy5, 1rnq, 1jn4, 1rnm, 1rbf, 1z3m, 1rnx, 1rob, 1rbn, 1rbx, 1eow, 1rbi, 1rbj, 1dfj, 1rsm, 1kf5, 1xps, 1rat, 1fev, 2aas, 1rhb, 1j80, 3srn, 1b6v, 1fs3, 1rpg, 1z6s, 1kf8, 1rtb, 4rsk, 1bzq, 9rsa, 1bel, 1kf4, 1kf7, 1rbw, 9rat, 1eie, 1rpf, 1o0m, 1c8w, 1rnc, 1rca, 1c0c, 1jvt, 3rsd, 1xpt, 1rbb, 2blz, 3rsp, 1ssc, 8rat, 2apq, 1j7z, 1w4o, 1rbd, 1rnz, 1jvv, 1rar, 1kf3, 1z3l, 1aqp, 1rbh, 1rbg, 1o0n, 1js0, 3rsk, 1ssa, 1cjr, 1eic, 1d5d, 1ymn, 1j81, 1rnw, 2w5k, 1rph, 2rns, 1rta, 1rnu, 1rny, 1z3p, 1gv7, 1rcn, 1rnv, 4rat, 1w4p, 4rsd, 1a5p, 1wbu, 1rha, 1ras, 2blp, 1rnd, 1kf2, 1d5h, 1srn, 2rat, 1d5e, 1izp, 2w5g, 1o0f, 1izr, 1c9x, 2rln, 4srn, 1c9v, 1u1b, 5rat, 1ruv, 1rbc, 2w5i, 1afl, 1z6d, 1rbe, 1a5q, 1kh8, 1lsq, 1jvu, 1a2w, 3rn3, 3rat
Activity:	Pancreatic ribonuclease, with EC number 3.1.27.5
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RNAS1_BOVIN] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Ribonuclease A is the archetype of a functionally diverse superfamily of vertebrate-specific ribonucleases. Inhibitors of its action have potential use in the elucidation of the in vivo roles of these enzymes and in the treatment of pathologies associated therewith. Derivatives of adenosine 5'-pyrophosphate are the most potent nucleotide-based inhibitors known. Here, we use X-ray crystallography to visualize the binding of four naturally-occurring derivatives that contain 5'-pyrophosphate-linked extensions. 5'-ATP binds with the adenine occupying the B(2) subsite in the manner of an RNA substrate but with the gamma-phosphate at the P(1) subsite. Diadenosine triphosphate (Ap(3)A) binds with the adenine in syn conformation, the beta-phosphate as the principal P(1) subsite ligand and without order beyond the gamma-phosphate. NADPH and NADP(+) bind with the adenine stacked against an alternative rotamer of His119, the 2'-phosphate at the P(1) subsite and without order beyond the 5'-alpha-phosphate. We also present the structure of the complex formed with pyrophosphate ion. The structural data enable existing kinetic data on the binding of these compounds to a variety of ribonucleases to be rationalized and suggest that as the complexity of the 5'-linked extension increases, the need to avoid unfavorable contacts places limitations on the number of possible binding modes. (c) 2009 Wiley Periodicals, Inc. Biopolymers, 2009.

Influence of naturally-occurring 5'-pyrophosphate-linked substituents on the binding of adenylic inhibitors to ribonuclease A: An X-ray crystallographic study.,Holloway DE, Chavali GB, Leonidas DD, Baker MD, Acharya KR Biopolymers. 2009 Feb 3. PMID:19191310^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ delCardayre SB, Ribo M, Yokel EM, Quirk DJ, Rutter WJ, Raines RT. Engineering ribonuclease A: production, purification and characterization of wild-type enzyme and mutants at Gln11. Protein Eng. 1995 Mar;8(3):261-73. PMID:7479688
↑ Holloway DE, Chavali GB, Leonidas DD, Baker MD, Acharya KR. Influence of naturally-occurring 5'-pyrophosphate-linked substituents on the binding of adenylic inhibitors to ribonuclease A: An X-ray crystallographic study. Biopolymers. 2009 Feb 3. PMID:19191310 doi:10.1002/bip.21158

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2w5m"

@@ Line 5: / Line 5: @@
 <table><tr><td colspan='2'>[[2w5m]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W5M OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2W5M FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ssb|1ssb]], [[1afu|1afu]], [[1w4q|1w4q]], [[1c0b|1c0b]], [[6rat|6rat]], [[1ymr|1ymr]], [[1o0o|1o0o]], [[8rsa|8rsa]], [[5rsa|5rsa]], [[1rno|1rno]], [[7rat|7rat]], [[2w5l|2w5l]], [[1izq|1izq]], [[1eid|1eid]], [[1cjq|1cjq]], [[1eos|1eos]], [[1rnn|1rnn]], [[1j82|1j82]], [[1qhc|1qhc]], [[1ymw|1ymw]], [[1o0h|1o0h]], [[1afk|1afk]], [[1f0v|1f0v]], [[1dy5|1dy5]], [[1rnq|1rnq]], [[1jn4|1jn4]], [[1rnm|1rnm]], [[1rbf|1rbf]], [[1z3m|1z3m]], [[1rnx|1rnx]], [[1rob|1rob]], [[1rbn|1rbn]], [[1rbx|1rbx]], [[1eow|1eow]], [[1rbi|1rbi]], [[1rbj|1rbj]], [[1dfj|1dfj]], [[1rsm|1rsm]], [[1kf5|1kf5]], [[1xps|1xps]], [[1rat|1rat]], [[1fev|1fev]], [[2aas|2aas]], [[1rhb|1rhb]], [[1j80|1j80]], [[3srn|3srn]], [[1b6v|1b6v]], [[1fs3|1fs3]], [[1rpg|1rpg]], [[1z6s|1z6s]], [[1kf8|1kf8]], [[1rtb|1rtb]], [[4rsk|4rsk]], [[1bzq|1bzq]], [[9rsa|9rsa]], [[1bel|1bel]], [[1kf4|1kf4]], [[1kf7|1kf7]], [[1rbw|1rbw]], [[9rat|9rat]], [[1eie|1eie]], [[1rpf|1rpf]], [[1o0m|1o0m]], [[1c8w|1c8w]], [[1rnc|1rnc]], [[1rca|1rca]], [[1c0c|1c0c]], [[1jvt|1jvt]], [[3rsd|3rsd]], [[1xpt|1xpt]], [[1rbb|1rbb]], [[2blz|2blz]], [[3rsp|3rsp]], [[1ssc|1ssc]], [[8rat|8rat]], [[2apq|2apq]], [[1j7z|1j7z]], [[1w4o|1w4o]], [[1rbd|1rbd]], [[1rnz|1rnz]], [[1jvv|1jvv]], [[1rar|1rar]], [[1kf3|1kf3]], [[1z3l|1z3l]], [[1aqp|1aqp]], [[1rbh|1rbh]], [[1rbg|1rbg]], [[1o0n|1o0n]], [[1js0|1js0]], [[3rsk|3rsk]], [[1ssa|1ssa]], [[1cjr|1cjr]], [[1eic|1eic]], [[1d5d|1d5d]], [[1ymn|1ymn]], [[1j81|1j81]], [[1rnw|1rnw]], [[2w5k|2w5k]], [[1rph|1rph]], [[2rns|2rns]], [[1rta|1rta]], [[1rnu|1rnu]], [[1rny|1rny]], [[1z3p|1z3p]], [[1gv7|1gv7]], [[1rcn|1rcn]], [[1rnv|1rnv]], [[4rat|4rat]], [[1w4p|1w4p]], [[4rsd|4rsd]], [[1a5p|1a5p]], [[1wbu|1wbu]], [[1rha|1rha]], [[1ras|1ras]], [[2blp|2blp]], [[1rnd|1rnd]], [[1kf2|1kf2]], [[1d5h|1d5h]], [[1srn|1srn]], [[2rat|2rat]], [[1d5e|1d5e]], [[1izp|1izp]], [[2w5g|2w5g]], [[1o0f|1o0f]], [[1izr|1izr]], [[1c9x|1c9x]], [[2rln|2rln]], [[4srn|4srn]], [[1c9v|1c9v]], [[1u1b|1u1b]], [[5rat|5rat]], [[1ruv|1ruv]], [[1rbc|1rbc]], [[2w5i|2w5i]], [[1afl|1afl]], [[1z6d|1z6d]], [[1rbe|1rbe]], [[1a5q|1a5q]], [[1kh8|1kh8]], [[1lsq|1lsq]], [[1jvu|1jvu]], [[1a2w|1a2w]], [[3rn3|3rn3]], [[3rat|3rat]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ssb|1ssb]], [[1afu|1afu]], [[1w4q|1w4q]], [[1c0b|1c0b]], [[6rat|6rat]], [[1ymr|1ymr]], [[1o0o|1o0o]], [[8rsa|8rsa]], [[5rsa|5rsa]], [[1rno|1rno]], [[7rat|7rat]], [[2w5l|2w5l]], [[1izq|1izq]], [[1eid|1eid]], [[1cjq|1cjq]], [[1eos|1eos]], [[1rnn|1rnn]], [[1j82|1j82]], [[1qhc|1qhc]], [[1ymw|1ymw]], [[1o0h|1o0h]], [[1afk|1afk]], [[1f0v|1f0v]], [[1dy5|1dy5]], [[1rnq|1rnq]], [[1jn4|1jn4]], [[1rnm|1rnm]], [[1rbf|1rbf]], [[1z3m|1z3m]], [[1rnx|1rnx]], [[1rob|1rob]], [[1rbn|1rbn]], [[1rbx|1rbx]], [[1eow|1eow]], [[1rbi|1rbi]], [[1rbj|1rbj]], [[1dfj|1dfj]], [[1rsm|1rsm]], [[1kf5|1kf5]], [[1xps|1xps]], [[1rat|1rat]], [[1fev|1fev]], [[2aas|2aas]], [[1rhb|1rhb]], [[1j80|1j80]], [[3srn|3srn]], [[1b6v|1b6v]], [[1fs3|1fs3]], [[1rpg|1rpg]], [[1z6s|1z6s]], [[1kf8|1kf8]], [[1rtb|1rtb]], [[4rsk|4rsk]], [[1bzq|1bzq]], [[9rsa|9rsa]], [[1bel|1bel]], [[1kf4|1kf4]], [[1kf7|1kf7]], [[1rbw|1rbw]], [[9rat|9rat]], [[1eie|1eie]], [[1rpf|1rpf]], [[1o0m|1o0m]], [[1c8w|1c8w]], [[1rnc|1rnc]], [[1rca|1rca]], [[1c0c|1c0c]], [[1jvt|1jvt]], [[3rsd|3rsd]], [[1xpt|1xpt]], [[1rbb|1rbb]], [[2blz|2blz]], [[3rsp|3rsp]], [[1ssc|1ssc]], [[8rat|8rat]], [[2apq|2apq]], [[1j7z|1j7z]], [[1w4o|1w4o]], [[1rbd|1rbd]], [[1rnz|1rnz]], [[1jvv|1jvv]], [[1rar|1rar]], [[1kf3|1kf3]], [[1z3l|1z3l]], [[1aqp|1aqp]], [[1rbh|1rbh]], [[1rbg|1rbg]], [[1o0n|1o0n]], [[1js0|1js0]], [[3rsk|3rsk]], [[1ssa|1ssa]], [[1cjr|1cjr]], [[1eic|1eic]], [[1d5d|1d5d]], [[1ymn|1ymn]], [[1j81|1j81]], [[1rnw|1rnw]], [[2w5k|2w5k]], [[1rph|1rph]], [[2rns|2rns]], [[1rta|1rta]], [[1rnu|1rnu]], [[1rny|1rny]], [[1z3p|1z3p]], [[1gv7|1gv7]], [[1rcn|1rcn]], [[1rnv|1rnv]], [[4rat|4rat]], [[1w4p|1w4p]], [[4rsd|4rsd]], [[1a5p|1a5p]], [[1wbu|1wbu]], [[1rha|1rha]], [[1ras|1ras]], [[2blp|2blp]], [[1rnd|1rnd]], [[1kf2|1kf2]], [[1d5h|1d5h]], [[1srn|1srn]], [[2rat|2rat]], [[1d5e|1d5e]], [[1izp|1izp]], [[2w5g|2w5g]], [[1o0f|1o0f]], [[1izr|1izr]], [[1c9x|1c9x]], [[2rln|2rln]], [[4srn|4srn]], [[1c9v|1c9v]], [[1u1b|1u1b]], [[5rat|5rat]], [[1ruv|1ruv]], [[1rbc|1rbc]], [[2w5i|2w5i]], [[1afl|1afl]], [[1z6d|1z6d]], [[1rbe|1rbe]], [[1a5q|1a5q]], [[1kh8|1kh8]], [[1lsq|1lsq]], [[1jvu|1jvu]], [[1a2w|1a2w]], [[3rn3|3rn3]], [[3rat|3rat]]</div></td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] </span></td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2w5m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w5m OCA], [http://pdbe.org/2w5m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2w5m RCSB], [http://www.ebi.ac.uk/pdbsum/2w5m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2w5m ProSAT]</span></td></tr>

2w5m

From Proteopedia

Revision as of 05:01, 19 November 2020

RNASE A-PYROPHOSPHATE ION COMPLEX

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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