4a3n

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of HMG-BOX of Human SOX17

Structural highlights

4a3n is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.4Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

SOX17_HUMAN Defects in SOX17 are the cause of vesicoureteral reflux type 3 (VUR3) [MIM:613674. VUR3 is a disease belonging to the group of congenital anomalies of the kidney and urinary tract. It is characterized by the reflux of urine from the bladder into the ureters and sometimes into the kidneys, and is a risk factor for urinary tract infections. Primary disease results from a developmental defect of the ureterovesical junction. In combination with intrarenal reflux, the resulting inflammatory reaction may result in renal injury or scarring, also called reflux nephropathy. Extensive renal scarring impairs renal function and may predispose patients to hypertension, proteinuria, renal insufficiency and end-stage renal disease.^[1]

Function

SOX17_HUMAN Acts as transcription regulator that binds target promoter DNA and bends the DNA. Binds to the sequences 5'-AACAAT-'3 or 5'-AACAAAG-3'. Modulates transcriptional regulation via WNT3A. Inhibits Wnt signaling. Promotes degradation of activated CTNNB1. Plays a key role in the regulation of embryonic development. Required for normal looping of the embryonic heart tube. Required for normal development of the definitive gut endoderm. Probable transcriptional activator in the premeiotic germ cells (By similarity).

Publication Abstract from PubMed

Sry-related box (Sox) transcription factors share a conserved high-mobility-group box domain (HMG-domain) that binds DNA in the minor groove and bends DNA for further assembly of transcriptional machineries. During organogenesis, each member of the Sox family triggers a specific cell lineage differentiation, indicating that their interactions with DNA are different from each other. Therefore, investigating structural rearrangement of each Sox transcription factor HMG-domain upon binding to DNA would help to elucidate the distinctive molecular mechanism by which they interact with DNA. Previous studies have determined the crystal structures of Sox2 HMG-domain/DNA, Sox4 HMG-domain/DNA, Sox9 HMG-domain/DNA and Sox17 HMG-domain/DNA complexes. However, major gaps remain in the structural information on the Sox transcription factor HMG-domains. Here, we report the crystal structure of the human Sox17 HMG-domain alone at 2.4 A resolution. Comparing this structure and the structure of the mouse Sox17 HMG-domain/DNA complex provides structural understanding of the mechanism of Sox17 binding to DNA. Specifically, after electrostatic interactions attract Sox17 to DNA, Asn73, Ser99, and Trp106 form hydrogen bonds with DNA, Arg70, Lys80, Arg83, His94, and Asn95 on Sox17 undergo conformational changes and form hydrogen bonds with DNA, contributing to the electrostatic interaction between Sox17 and DNA.

Structural Basis of Human Transcription Factor Sry-related Box 17 Binding to DNA.,Gao N, Jiang W, Gao H, Cheng Z, Qian H, Si S, Xie Y Protein Pept Lett. 2012 Oct 11. PMID:23061670^[2]

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

References

↑ Gimelli S, Caridi G, Beri S, McCracken K, Bocciardi R, Zordan P, Dagnino M, Fiorio P, Murer L, Benetti E, Zuffardi O, Giorda R, Wells JM, Gimelli G, Ghiggeri GM. Mutations in SOX17 are associated with congenital anomalies of the kidney and the urinary tract. Hum Mutat. 2010 Dec;31(12):1352-9. doi: 10.1002/humu.21378. Epub 2010 Nov 9. PMID:20960469 doi:10.1002/humu.21378
↑ Gao N, Jiang W, Gao H, Cheng Z, Qian H, Si S, Xie Y. Structural Basis of Human Transcription Factor Sry-related Box 17 Binding to DNA. Protein Pept Lett. 2012 Oct 11. PMID:23061670

1 Structural highlights
2 Disease
3 Function
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4a3n"

@@ Line 3: / Line 3: @@
 <StructureSection load='4a3n' size='340' side='right'caption='[[4a3n]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4a3n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4A3N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4A3N FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4a3n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4A3N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4A3N FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 2.4&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=4a3n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4a3n OCA], [https://pdbe.org/4a3n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4a3n RCSB], [https://www.ebi.ac.uk/pdbsum/4a3n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4a3n ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[https://www.uniprot.org/uniprot/SOX17_HUMAN SOX17_HUMAN]] Defects in SOX17 are the cause of vesicoureteral reflux type 3 (VUR3) [MIM:[https://omim.org/entry/613674 613674]]. VUR3 is a disease belonging to the group of congenital anomalies of the kidney and urinary tract. It is characterized by the reflux of urine from the bladder into the ureters and sometimes into the kidneys, and is a risk factor for urinary tract infections. Primary disease results from a developmental defect of the ureterovesical junction. In combination with intrarenal reflux, the resulting inflammatory reaction may result in renal injury or scarring, also called reflux nephropathy. Extensive renal scarring impairs renal function and may predispose patients to hypertension, proteinuria, renal insufficiency and end-stage renal disease.<ref>PMID:20960469</ref>
+[https://www.uniprot.org/uniprot/SOX17_HUMAN SOX17_HUMAN] Defects in SOX17 are the cause of vesicoureteral reflux type 3 (VUR3) [MIM:[https://omim.org/entry/613674 613674]. VUR3 is a disease belonging to the group of congenital anomalies of the kidney and urinary tract. It is characterized by the reflux of urine from the bladder into the ureters and sometimes into the kidneys, and is a risk factor for urinary tract infections. Primary disease results from a developmental defect of the ureterovesical junction. In combination with intrarenal reflux, the resulting inflammatory reaction may result in renal injury or scarring, also called reflux nephropathy. Extensive renal scarring impairs renal function and may predispose patients to hypertension, proteinuria, renal insufficiency and end-stage renal disease.<ref>PMID:20960469</ref>
 == Function ==
-[[https://www.uniprot.org/uniprot/SOX17_HUMAN SOX17_HUMAN]] Acts as transcription regulator that binds target promoter DNA and bends the DNA. Binds to the sequences 5'-AACAAT-'3 or 5'-AACAAAG-3'. Modulates transcriptional regulation via WNT3A. Inhibits Wnt signaling. Promotes degradation of activated CTNNB1. Plays a key role in the regulation of embryonic development. Required for normal looping of the embryonic heart tube. Required for normal development of the definitive gut endoderm. Probable transcriptional activator in the premeiotic germ cells (By similarity).
+[https://www.uniprot.org/uniprot/SOX17_HUMAN SOX17_HUMAN] Acts as transcription regulator that binds target promoter DNA and bends the DNA. Binds to the sequences 5'-AACAAT-'3 or 5'-AACAAAG-3'. Modulates transcriptional regulation via WNT3A. Inhibits Wnt signaling. Promotes degradation of activated CTNNB1. Plays a key role in the regulation of embryonic development. Required for normal looping of the embryonic heart tube. Required for normal development of the definitive gut endoderm. Probable transcriptional activator in the premeiotic germ cells (By similarity).
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 25: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Gao, H]]
+[[Category: Gao H]]
-[[Category: Gao, N]]
+[[Category: Gao N]]
-[[Category: Qian, H]]
+[[Category: Qian H]]
-[[Category: Si, S]]
+[[Category: Si S]]
-[[Category: Xie, Y]]
+[[Category: Xie Y]]
-[[Category: Transcription]]

4a3n

From Proteopedia

Current revision

Crystal Structure of HMG-BOX of Human SOX17

Structural highlights

Disease

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox