2GYP - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   DIABETES MELLITUS DUE TO A FRUSTRATED SCHELLMAN MOTIF IN HNF-1A

Authors :   N. Narayana, N. B. Phillips, Q. X. Hua, W. Jia, M. A. Weiss

Date :   09 May 06 (Deposition) - 20 Mar 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (2x)
Biol. Unit 2: B  (2x)
Biol. Unit 3: A,B  (2x)

Keywords :   Energy Landscape, Gene Regulation, Protein Engineering, Protein Stability, Protein Structure, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Narayana, N. B. Phillips, Q. X. Hua, W. Jia, M. A. Weiss
Diabetes Mellitus Due To Misfolding Of A Beta-Cell Transcription Factor: Stereospecific Frustration Of A Schellman Motif In Hnf-1Alpha.
J. Mol. Biol. V. 362 414 2006
PubMed-ID: 16930618 | Reference-DOI: 10.1016/J.JMB.2006.06.086
(for further references see the PDB file header)

Molecule 1 - HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
	Chains	:	A, B
	Engineered	:	YES
	Fragment	:	DIMERIZATION DOMAIN
	Mutation	:	YES
	Other Details	:	THE SEQUENCE WAS CHEMCIALLY SYNTHESIZED. THE SOURCE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN).
	Synonym	:	HNF-1A, LIVER-SPECIFIC TRANSCRIPTION FACTOR LF-B1, LFB1, TRANSCRIPTION FACTOR 1, TCF-1
	Synthetic	:	YES

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A
Biological Unit 2 (2x)	:		B
Biological Unit 3 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	DAL	2	Mod. Amino Acid	D-ALANINE
2	NLE	2	Mod. Amino Acid	NORLEUCINE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	DAL	2	Mod. Amino Acid	D-ALANINE
2	NLE	2	Mod. Amino Acid	NORLEUCINE

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	DAL	2	Mod. Amino Acid	D-ALANINE
2	NLE	2	Mod. Amino Acid	NORLEUCINE

Biological Unit 3 (2, 8)

No.	Name	Count	Type	Full Name
1	DAL	4	Mod. Amino Acid	D-ALANINE
2	NLE	4	Mod. Amino Acid	NORLEUCINE

(no "Site" information available for 2GYP)

(no "SS Bond" information available for 2GYP)

(no "Cis Peptide Bond" information available for 2GYP)

Asymmetric Unit (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_010537	L	12	H	HNF1A_HUMAN	Disease (MODY3)	---	A B	L	12 45	H
2	UniProt	VAR_012483	G	20	R	HNF1A_HUMAN	Disease (MODY3)	---	A B	A	20 53	R
3	UniProt	VAR_007905	I	27	L	HNF1A_HUMAN	Polymorphism	1169288	A B	I	27 60	L
4	UniProt	VAR_010538	G	31	D	HNF1A_HUMAN	Disease (MODY3)	---	A B	G	31 64	D

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_010537	L	12	H	HNF1A_HUMAN	Disease (MODY3)	---	A A	L	12 45	H
2	UniProt	VAR_012483	G	20	R	HNF1A_HUMAN	Disease (MODY3)	---	A A	A	20 53	R
3	UniProt	VAR_007905	I	27	L	HNF1A_HUMAN	Polymorphism	1169288	A A	I	27 60	L
4	UniProt	VAR_010538	G	31	D	HNF1A_HUMAN	Disease (MODY3)	---	A A	G	31 64	D

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_010537	L	12	H	HNF1A_HUMAN	Disease (MODY3)	---	A B	L	12 45	H
2	UniProt	VAR_012483	G	20	R	HNF1A_HUMAN	Disease (MODY3)	---	A B	A	20 53	R
3	UniProt	VAR_007905	I	27	L	HNF1A_HUMAN	Polymorphism	1169288	A B	I	27 60	L
4	UniProt	VAR_010538	G	31	D	HNF1A_HUMAN	Disease (MODY3)	---	A B	G	31 64	D

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (4, 16)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_010537	L	12	H	HNF1A_HUMAN	Disease (MODY3)	---	A A/B	L	12 45	H
2	UniProt	VAR_012483	G	20	R	HNF1A_HUMAN	Disease (MODY3)	---	A A/B	A	20 53	R
3	UniProt	VAR_007905	I	27	L	HNF1A_HUMAN	Polymorphism	1169288	A A/B	I	27 60	L
4	UniProt	VAR_010538	G	31	D	HNF1A_HUMAN	Disease (MODY3)	---	A A/B	G	31 64	D

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 2GYP)

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000257555	1a	ENSE00001893688	chr12:121416346-121416897	552	HNF1A_HUMAN	1-109	109	2	A:1-33 B:34-66	33 33
1.2	ENST00000257555	2	ENSE00000756493	chr12:121426636-121426835	200	HNF1A_HUMAN	109-176	68	0	-	-
1.3	ENST00000257555	3	ENSE00000756490	chr12:121431323-121431509	187	HNF1A_HUMAN	176-238	63	0	-	-
1.4	ENST00000257555	4	ENSE00000564735	chr12:121431967-121432208	242	HNF1A_HUMAN	238-319	82	0	-	-
1.5	ENST00000257555	5	ENSE00000756487	chr12:121434065-121434216	152	HNF1A_HUMAN	319-369	51	0	-	-
1.6a	ENST00000257555	6a	ENSE00000940088	chr12:121434344-121434545	202	HNF1A_HUMAN	370-437	68	0	-	-
1.6e	ENST00000257555	6e	ENSE00000756464	chr12:121435277-121435468	192	HNF1A_HUMAN	437-501	65	0	-	-
1.7	ENST00000257555	7	ENSE00000756456	chr12:121437071-121437192	122	HNF1A_HUMAN	501-541	41	0	-	-
1.8	ENST00000257555	8	ENSE00000756450	chr12:121437286-121437430	145	HNF1A_HUMAN	542-590	49	0	-	-
1.9a	ENST00000257555	9a	ENSE00000835338	chr12:121438868-121440899	2032	HNF1A_HUMAN	590-631	42	0	-	-

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:33
 aligned with HNF1A_HUMAN | P20823 from UniProtKB/Swiss-Prot  Length:631

    Alignment length:33
                                    10        20        30   
           HNF1A_HUMAN    1 MVSKLSQLQTELLAALLESGLSKEALIQALGEP 33
               SCOP domains --------------------------------- SCOP domains
               CATH domains --------------------------------- CATH domains
               Pfam domains --------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------- PROSITE
               Transcript 1 Exon 1.1a  PDB: A:1-33            Transcript 1
                  2gyp A  1 lVSKLSQLQTELLAALLESaLSKEALIQALGEW 33
                            |       10        20        30   
                            |                 20-DAL         
                            1-NLE

Chain B from PDB  Type:PROTEIN  Length:33
 aligned with HNF1A_HUMAN | P20823 from UniProtKB/Swiss-Prot  Length:631

    Alignment length:33
                                    10        20        30   
           HNF1A_HUMAN    1 MVSKLSQLQTELLAALLESGLSKEALIQALGEP 33
               SCOP domains --------------------------------- SCOP domains
               CATH domains --------------------------------- CATH domains
               Pfam domains --------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------H-------R------L---D-- SAPs(SNPs)
                    PROSITE --------------------------------- PROSITE
               Transcript 1 Exon 1.1a  PDB: B:34-66           Transcript 1
                  2gyp B 34 lVSKLSQLQTELLAALLESaLSKEALIQALGEW 66
                            |       43        53        63   
                           34-NLE             53-DAL

Legend:		→ Mismatch	(orange background)
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		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 2GYP)

(no "CATH Domain" information available for 2GYP)

(no "Pfam Domain" information available for 2GYP)

Asymmetric Unit(hide GO term definitions)

Chain A,B (HNF1A_HUMAN | P20823)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0044212	transcription regulatory region DNA binding	Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
	GO:0001077	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
biological process
	GO:0042593	glucose homeostasis	Any process involved in the maintenance of an internal steady state of glucose within an organism or cell.
	GO:0046323	glucose import	The directed movement of the hexose monosaccharide glucose into a cell or organelle.
	GO:0030073	insulin secretion	The regulated release of proinsulin from secretory granules (B granules) in the B cells of the pancreas; accompanied by cleavage of proinsulin to form mature insulin.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0060261	positive regulation of transcription initiation from RNA polymerase II promoter	Any process that increases the rate, frequency or extent of a process involved in starting transcription from an RNA polymerase II promoter.
	GO:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0035565	regulation of pronephros size	Any process that modulates the size of a pronephric kidney.
	GO:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0035623	renal glucose absorption	A renal system process in which glucose is taken up from the collecting ducts and proximal and distal loops of the nephron. In non-mammalian species, absorption may occur in related structures.
	GO:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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	2gyp
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	HNF1A_HUMAN \| P20823
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	HNF1A_HUMAN \| P20823	:	1ic8

1g2y	THE SAME PROTEIN WITHOUT MODIFICATION AT POSITION 20 AND HAS SE-MET AT POSITION 12
1g2z	THE SAME PROTEIN WITHOUT MODIFICATION AT POSITION 20 AND HAS SE-MET AT POSITION 13
1g39	NATIVE PROTEIN.
1jb6	THE SAME PROTEIN WITHOUT MODIFICATION AT POSITION 20 AND HAS SE-MET AT POSITION 13

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 8)

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Exons (1, 2)

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Gene Ontology (23, 23)

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