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| - | ==HYDROGENASE MATURATION PROTEIN HYPF "ACYLPHOSPHATASE-LIKE" N-TERMINAL DOMAIN (HYPF-ACP) IN COMPLEX WITH SULFATE== | + | |
| - | <StructureSection load='1gxt' size='340' side='right' caption='[[1gxt]], [[Resolution|resolution]] 1.27Å' scene=''> | + | ==Hydrogenase Maturation Protein HypF "acylphosphatase-like" N-terminal domain (HypF-ACP) in complex with Sulfate== |
| | + | <StructureSection load='1gxt' size='340' side='right'caption='[[1gxt]], [[Resolution|resolution]] 1.27Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1gxt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GXT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GXT FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1gxt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GXT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GXT FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.27Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1gxu|1gxu]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1gxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gxt OCA], [http://pdbe.org/1gxt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gxt RCSB], [http://www.ebi.ac.uk/pdbsum/1gxt PDBsum]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1gxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gxt OCA], [https://pdbe.org/1gxt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gxt RCSB], [https://www.ebi.ac.uk/pdbsum/1gxt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gxt ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/HYPF_ECOLI HYPF_ECOLI]] Along with HypE, it catalyzes the synthesis of the CN ligands of the active site iron of [NiFe]-hydrogenases using carbamoylphosphate as a substrate. It functions as a carbamoyl transferase using carbamoylphosphate as a substrate and transferring the carboxamido moiety in an ATP-dependent reaction to the thiolate of the C-terminal cysteine of HypE yielding a protein-S-carboxamide.<ref>PMID:8661925</ref> <ref>PMID:12377778</ref> <ref>PMID:15291820</ref> <ref>PMID:15504408</ref> | + | [https://www.uniprot.org/uniprot/HYPF_ECOLI HYPF_ECOLI] Along with HypE, it catalyzes the synthesis of the CN ligands of the active site iron of [NiFe]-hydrogenases using carbamoylphosphate as a substrate. It functions as a carbamoyl transferase using carbamoylphosphate as a substrate and transferring the carboxamido moiety in an ATP-dependent reaction to the thiolate of the C-terminal cysteine of HypE yielding a protein-S-carboxamide.<ref>PMID:8661925</ref> <ref>PMID:12377778</ref> <ref>PMID:15291820</ref> <ref>PMID:15504408</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gx/1gxt_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gx/1gxt_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | ==See Also== | | ==See Also== |
| - | *[[HypA-HypB-HypC-HypD-HypE-HypF|HypA-HypB-HypC-HypD-HypE-HypF]] | + | *[[HypA%2C HypB%2C HypC%2C HypD%2C HypE and HypF 3D structures|HypA%2C HypB%2C HypC%2C HypD%2C HypE and HypF 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| - | [[Category: Bolognesi, M]] | + | [[Category: Large Structures]] |
| - | [[Category: Bucciantini, M]] | + | [[Category: Bolognesi M]] |
| - | [[Category: Ramponi, G]] | + | [[Category: Bucciantini M]] |
| - | [[Category: Rosano, C]] | + | [[Category: Ramponi G]] |
| - | [[Category: Stefani, M]] | + | [[Category: Rosano C]] |
| - | [[Category: Zuccotti, S]] | + | [[Category: Stefani M]] |
| - | [[Category: Acylphosphatase]]
| + | [[Category: Zuccotti S]] |
| - | [[Category: Fibril formation]]
| + | |
| - | [[Category: Hydrogenase maturation]]
| + | |
| - | [[Category: Phosphatase]]
| + | |
| - | [[Category: Zinc-finger]]
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| Structural highlights
Function
HYPF_ECOLI Along with HypE, it catalyzes the synthesis of the CN ligands of the active site iron of [NiFe]-hydrogenases using carbamoylphosphate as a substrate. It functions as a carbamoyl transferase using carbamoylphosphate as a substrate and transferring the carboxamido moiety in an ATP-dependent reaction to the thiolate of the C-terminal cysteine of HypE yielding a protein-S-carboxamide.[1] [2] [3] [4]
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
[NiFe]-hydrogenases require a set of complementary and regulatory proteins for correct folding and maturation processes. One of the essential regulatory proteins, HypF (82kDa) contains a N-terminal acylphosphatase (ACT)-like domain, a sequence motif shared with enzymes catalyzing O-carbamoylation, and two zinc finger motifs similar to those found in the DnaJ chaperone. The HypF acylphosphatase domain is thought to support the conversion of carbamoylphosphate into CO and CN(-), promoting coordination of these ligands to the hydrogenase metal cluster. It has been shown recently that the HypF N-terminal domain can aggregate in vitro to yield fibrils matching those formed by proteins linked to amyloid diseases. The 1.27A resolution HypF acylphosphatase domain crystal structure (residues 1-91; R-factor 13.1%) shows a domain fold of betaalphabetabetaalphabeta topology, as observed in mammalian acylphosphatases specifically catalyzing the hydrolysis of the carboxyl-phosphate bonds in acylphosphates. The HypF N-terminal domain can be assigned to the ferredoxin structural superfamily, to which RNA-binding domains of small nuclear ribonucleoproteins and some metallochaperone proteins belong. Additionally, the HypF N-terminal domain displays an intriguing structural relationship to the recently discovered ACT domains. The structures of different HypF acylphosphatase domain complexes show a phosphate binding cradle comparable to the P-loop observed in unrelated phosphatase families. On the basis of the catalytic mechanism proposed for acylphosphatases, whereby residues Arg23 and Asn41 would support substrate orientation and the nucleophilic attack of a water molecule on the phosphate group, fine structural features of the HypF N-terminal domain putative active site region may account for the lack of acylphosphatase activity observed for the expressed domain. The crystallographic analyses here reported were undertaken to shed light on the molecular bases of inactivity, folding, misfolding and aggregation of the HypF N-terminal acylphosphatase domain.
Crystal structure and anion binding in the prokaryotic hydrogenase maturation factor HypF acylphosphatase-like domain.,Rosano C, Zuccotti S, Bucciantini M, Stefani M, Ramponi G, Bolognesi M J Mol Biol. 2002 Aug 30;321(5):785-96. PMID:12206761[5]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Maier T, Binder U, Bock A. Analysis of the hydA locus of Escherichia coli: two genes (hydN and hypF) involved in formate and hydrogen metabolism. Arch Microbiol. 1996 May;165(5):333-41. PMID:8661925
- ↑ Paschos A, Bauer A, Zimmermann A, Zehelein E, Bock A. HypF, a carbamoyl phosphate-converting enzyme involved in [NiFe] hydrogenase maturation. J Biol Chem. 2002 Dec 20;277(51):49945-51. Epub 2002 Oct 10. PMID:12377778 doi:http://dx.doi.org/10.1074/jbc.M204601200
- ↑ Blokesch M, Paschos A, Bauer A, Reissmann S, Drapal N, Bock A. Analysis of the transcarbamoylation-dehydration reaction catalyzed by the hydrogenase maturation proteins HypF and HypE. Eur J Biochem. 2004 Aug;271(16):3428-36. PMID:15291820 doi:http://dx.doi.org/10.1111/j.1432-1033.2004.04280.x
- ↑ Blokesch M, Albracht SP, Matzanke BF, Drapal NM, Jacobi A, Bock A. The complex between hydrogenase-maturation proteins HypC and HypD is an intermediate in the supply of cyanide to the active site iron of [NiFe]-hydrogenases. J Mol Biol. 2004 Nov 12;344(1):155-67. PMID:15504408 doi:http://dx.doi.org/10.1016/j.jmb.2004.09.040
- ↑ Rosano C, Zuccotti S, Bucciantini M, Stefani M, Ramponi G, Bolognesi M. Crystal structure and anion binding in the prokaryotic hydrogenase maturation factor HypF acylphosphatase-like domain. J Mol Biol. 2002 Aug 30;321(5):785-96. PMID:12206761
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