This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


4rzb

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (12:57, 1 March 2024) (edit) (undo)
 
(One intermediate revision not shown.)
Line 3: Line 3:
<StructureSection load='4rzb' size='340' side='right'caption='[[4rzb]], [[Resolution|resolution]] 1.86&Aring;' scene=''>
<StructureSection load='4rzb' size='340' side='right'caption='[[4rzb]], [[Resolution|resolution]] 1.86&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4rzb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RZB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RZB FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4rzb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RZB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RZB FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=NFQ:N-[(E)-IMINOMETHYL]-L-ASPARTIC+ACID'>NFQ</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.863&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3mdw|3mdw]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=NFQ:N-[(E)-IMINOMETHYL]-L-ASPARTIC+ACID'>NFQ</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PA5106 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</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=4rzb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzb OCA], [https://pdbe.org/4rzb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rzb RCSB], [https://www.ebi.ac.uk/pdbsum/4rzb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rzb ProSAT]</span></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=4rzb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzb OCA], [http://pdbe.org/4rzb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rzb RCSB], [http://www.ebi.ac.uk/pdbsum/4rzb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rzb ProSAT]</span></td></tr>
+
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/HUTF_PSEAE HUTF_PSEAE] Catalyzes the hydrolysis of N-formimino-L-glutamate to N-formyl-L-glutamate and ammonia.<ref>PMID:16475788</ref> <ref>PMID:17128965</ref>
-
N-Formimino-l-glutamate iminohydrolase (HutF), from Pseudomonas aeruginosa with a locus tag of Pa5106 ( gi|15600299 ), is a member of the amidohydrolase superfamily. This enzyme catalyzes the deamination of N-formimino-l-glutamate to N-formyl-l-glutamate and ammonia in the histidine degradation pathway. The crystal structure of Pa5106 was determined in the presence of the inhibitors N-formimino-l-aspartate and N-guanidino-l-glutaric acid at resolutions of 1.9 and 1.4 A, respectively. The structure of an individual subunit is composed of two domains with the larger domain folding as a distorted (beta/alpha)8-barrel. The (beta/alpha)8-barrel domain is composed of eight beta-strands flanked by 11 alpha-helices, whereas the smaller domain is made up of eight beta-strands. The active site of Pa5106 contains a single zinc atom that is coordinated by His-56, His-58, His-232, and Asp-320. The nucleophilic solvent water molecule coordinates with the zinc atom at a distance of 2.0 A and is hydrogen bonded to Asp-320 and His-269. The alpha-carboxylate groups of both inhibitors are hydrogen bonded to the imidazole moiety of His-206, the hydroxyl group of Tyr-121, and the side chain amide group of Gln-61. The side chain carboxylate groups of the two inhibitors are ion-paired with the guanidino groups of Arg-209 and Arg-82. Computational docking of high-energy tetrahedral intermediate forms of the substrate, N-formimino-l-glutamate, to the three-dimensional structure of Pa5106 suggests that this compound likely undergoes a re-faced nucleophilic attack at the formimino group by the metal-bound hydroxide. A catalytic mechanism of the reaction catalyzed by Pa5106 is proposed.
+
-
 
+
-
Structure of N-Formimino-l-glutamate Iminohydrolase from Pseudomonas aeruginosa.,Fedorov AA, Marti-Arbona R, Nemmara VV, Hitchcock D, Fedorov EV, Almo SC, Raushel FM Biochemistry. 2015 Jan 16. PMID:25559274<ref>PMID:25559274</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 4rzb" style="background-color:#fffaf0;"></div>
+
== References ==
== References ==
<references/>
<references/>
Line 23: Line 15:
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Pseae]]
+
[[Category: Pseudomonas aeruginosa PAO1]]
-
[[Category: Almo, S C]]
+
[[Category: Almo SC]]
-
[[Category: Fedorov, A A]]
+
[[Category: Fedorov AA]]
-
[[Category: Fedorov, E V]]
+
[[Category: Fedorov EV]]
-
[[Category: Marti-Arbona, R]]
+
[[Category: Marti-Arbona R]]
-
[[Category: Raushel, F M]]
+
[[Category: Raushel FM]]
-
[[Category: Amidohydrolase fold]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: N-formimino-l-aspartate]]
+
-
[[Category: N-formimino-l-glutamate iminohydrolase]]
+

Current revision

The structure of N-formimino-L-Glutamate Iminohydrolase from Pseudomonas aeruginosa complexed with N-formimino-L-Aspartate, SOAKED WITH MERCURY

PDB ID 4rzb

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4rzb"
Personal tools