2XUM - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   FACTOR INHIBITING HIF (FIH) Q239H MUTANT IN COMPLEX WITH ZN(II), NOG AND ASP-SUBSTRATE PEPTIDE (20-MER)

Authors :   R. Chowdhury, M. A. Mcdonough, C. J. Schofield

Date :   19 Oct 10 (Deposition) - 22 Dec 10 (Release) - 18 Mar 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Oxidoreductase-Peptide Complex, Non-Heme, Dioxygenase, Oxygenase, Hypoxia, Metal-Binding, Helix-Loop-Helix-Beta, Facial Triad Signaling, Beta-Hydroxylation, Transcription Activator/Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Yang, W. Ge, R. Chowdhury, T. D. W. Claridge, H. B. Kramer, B. Schmierer, M. A. Mcdonough, L. Gong, B. M. Kessler, P. J. Ratcliffe, M. L. Coleman, C. J. Schofield
Asparagine And Aspartate Hydroxylation Of The Cytoskeletal Ankyrin Family Is Catalyzed By Factor-Inhibiting Hypoxia- Inducible Factor.
J. Biol. Chem. V. 286 7648 2011
PubMed-ID: 21177872 | Reference-DOI: 10.1074/JBC.M110.193540
(for further references see the PDB file header)

Molecule 1 - HYPOXIA-INDUCIBLE FACTOR 1-ALPHA INHIBITOR
	Chains	:	A
	EC Number	:	1.14.11.16
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET28A(+)
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	FACTOR INHIBITING HIF-1, FIH-1, HYPOXIA-INDUCIBLE FACTOR ASPARAGINE HYDROXYLASE

Molecule 2 - ASP-SUBSTRATE PEPTIDE 2
	Chains	:	S
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Other Details	:	BASED ON BIOLOGICAL SEQUENCE
	Synthetic	:	YES

		1	2
Asymmetric Unit	:	A	S
Biological Unit 1 (2x)	:	A	S
Biological Unit 2 (1x)	:	A	S

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	OGA	1	Ligand/Ion	N-OXALYLGLYCINE
2	SO4	3	Ligand/Ion	SULFATE ION
3	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	OGA	2	Ligand/Ion	N-OXALYLGLYCINE
2	SO4	6	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	OGA	1	Ligand/Ion	N-OXALYLGLYCINE
2	SO4	3	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:199 , ASP A:201 , HIS A:279 , OGA A:601 , HOH A:2144	BINDING SITE FOR RESIDUE ZN A 501
2	AC2	SOFTWARE	TYR A:145 , LEU A:188 , THR A:196 , HIS A:199 , ASP A:201 , ASN A:205 , PHE A:207 , LYS A:214 , HIS A:279 , ILE A:281 , ASN A:294 , TRP A:296 , ZN A:501 , HOH A:2144	BINDING SITE FOR RESIDUE OGA A 601
3	AC3	SOFTWARE	ARG A:138 , GLY A:140 , GLU A:141 , GLU A:142	BINDING SITE FOR RESIDUE SO4 A 602
4	AC4	SOFTWARE	ARG A:143 , GLU A:192 , GLY A:193 , LEU A:285 , ASN A:286	BINDING SITE FOR RESIDUE SO4 A 603
5	AC5	SOFTWARE	LYS A:311 , ALA A:312 , HOH A:2146 , HOH A:2147	BINDING SITE FOR RESIDUE SO4 A 604

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

Asymmetric Unit

No.	Residues
1	Tyr A:308	-	Pro A:309

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051028	P	41	A	HIF1N_HUMAN	Polymorphism	2295778	A	P	41	A

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

Biological Unit 1 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051028	P	41	A	HIF1N_HUMAN	Polymorphism	2295778	A	P	41	A

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051028	P	41	A	HIF1N_HUMAN	Polymorphism	2295778	A	P	41	A

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	JMJC	PS51184	JmjC domain profile.	HIF1N_HUMAN	142-312	1	A:142-312

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	JMJC	PS51184	JmjC domain profile.	HIF1N_HUMAN	142-312	2	A:142-312

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	JMJC	PS51184	JmjC domain profile.	HIF1N_HUMAN	142-312	1	A:142-312

Asymmetric Unit (8, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2b	ENST00000299163	2b	ENSE00001695622	chr10:102295616-102295892	277	HIF1N_HUMAN	1-59	59	1	A:1-59	59
1.3b	ENST00000299163	3b	ENSE00001100126	chr10:102296168-102296418	251	HIF1N_HUMAN	60-143	84	1	A:60-143	84
1.4b	ENST00000299163	4b	ENSE00001100124	chr10:102300391-102300539	149	HIF1N_HUMAN	143-193	51	1	A:143-193	51
1.5a	ENST00000299163	5a	ENSE00001100127	chr10:102304708-102304853	146	HIF1N_HUMAN	193-241	49	1	A:193-241	49
1.6b	ENST00000299163	6b	ENSE00001100128	chr10:102305700-102305806	107	HIF1N_HUMAN	242-277	36	1	A:242-277	36
1.7	ENST00000299163	7	ENSE00001100132	chr10:102306275-102306338	64	HIF1N_HUMAN	277-298	22	1	A:277-298	22
1.8b	ENST00000299163	8b	ENSE00001100130	chr10:102306897-102307007	111	HIF1N_HUMAN	299-335	37	1	A:299-335	37
1.9b	ENST00000299163	9b	ENSE00001212367	chr10:102307850-102309763	1914	HIF1N_HUMAN	336-349	14	1	A:336-349	14

Asymmetric Unit

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

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:349
 aligned with HIF1N_HUMAN | Q9NWT6 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:349
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340         
          HIF1N_HUMAN     1 MAATAAEAVASGSGEPREEAGALGPAWDESQLRSYSFPTRPIPRLSQSDPRAEELIENEEPVVLTDTNLVYPALKWDLEYLQENIGNGDFSVYSASTHKFLYYDEKKMANFQNFKPRSNREEMKFHEFVEKLQDIQQRGGEERLYLQQTLNDTVGRKIVMDFLGFNWNWINKQQGKRGWGQLTSNLLLIGMEGNVTPAHYDEQQNFFAQIKGYKRCILFPPDQFECLYPYPVHHPCDRQSQVDFDNPDYERFPNFQNVVGYETVVGPGDVLYIPMYWWHHIESLLNGGITITVNFWYKGAPTPKRIEYPLKAHQKVAIMRNIEKMLGEALGNPQEVGPLLNTMIKGRYN 349
               SCOP domains d2xuma_ A: Hypoxia-inducible factor HIF ihhibitor (FIH1)                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh........hhhhh....hhhhh......eee..ee...hhhhhhhhhh...eee.....hhhhhhhhhhhhhhhh....eeeeee......................eeeeeehhhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhh.hhhhhhhhhhhhh...eee.eeeee....eeeee....eeeeeeee..eeeeeehhhhhhhhh.......................hhhhhhh.eeeeee....eeee....eeeeee......eeeeeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------JMJC  PDB: A:142-312 UniProt: 142-312                                                                                                                                      ------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:1-59 UniProt: 1-59                       Exon 1.3b  PDB: A:60-143 UniProt: 60-143                                            -------------------------------------------------Exon 1.5a  PDB: A:193-241 UniProt: 193-241       Exon 1.6b  PDB: A:242-277           ---------------------Exon 1.8b  PDB: A:299-335            Exon 1.9b      Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------Exon 1.4b  PDB: A:143-193 UniProt: 143-193         -----------------------------------------------------------------------------------Exon 1.7              --------------------------------------------------- Transcript 1 (2)
                 2xum A   1 MAATAAEAVASGSGEPREEAGALGPAWDESQLRSYSFPTRPIPRLSQSDPRAEELIENEEPVVLTDTNLVYPALKWDLEYLQENIGNGDFSVYSASTHKFLYYDEKKMANFQNFKPRSNREEMKFHEFVEKLQDIQQRGGEERLYLQQTLNDTVGRKIVMDFLGFNWNWINKQQGKRGWGQLTSNLLLIGMEGNVTPAHYDEQQNFFAQIKGYKRCILFPPDQFECLYPYPVHHPCDRHSQVDFDNPDYERFPNFQNVVGYETVVGPGDVLYIPMYWWHHIESLLNGGITITVNFWYKGAPTPKRIEYPLKAHQKVAIMRNIEKMLGEALGNPQEVGPLLNTMIKGRYN 349
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340

Chain S from PDB  Type:PROTEIN  Length:18
                                                  
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author hhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
                 Transcript ------------------ Transcript
                 2xum S 790 EVVKLLLEHGADVDAQDK 807
                                   799

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: Double-stranded beta-helix (580)

Superfamily: Clavaminate synthase-like (197)

Family: Hypoxia-inducible factor HIF ihhibitor (FIH1) (26)

Protein domain: Hypoxia-inducible factor HIF ihhibitor (FIH1) (26)

Human (Homo sapiens) [TaxId: 9606] (26)

d2xuma_

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

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

Asymmetric Unit(hide GO term definitions)

Chain A (HIF1N_HUMAN | Q9NWT6)

molecular function
	GO:0051059	NF-kappaB binding	Interacting selectively and non-covalently with NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters.
	GO:0005112	Notch binding	Interacting selectively and non-covalently with the Notch (N) protein, a surface receptor.
	GO:0071532	ankyrin repeat binding	Interacting selectively and non-covalently with an ankyrin repeat of a protein. Ankyrin repeats are tandemly repeated modules of about 33 amino acids; each repeat folds into a helix-loop-helix structure with a beta-hairpin/loop region projecting out from the helices at a 90-degree angle, and repeats stack to form an L-shaped structure.
	GO:0031406	carboxylic acid binding	Interacting selectively and non-covalently with a carboxylic acid, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
	GO:0048037	cofactor binding	Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
	GO:0051213	dioxygenase activity	Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016706	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors	Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor.
	GO:0019826	oxygen sensor activity	Interacting selectively and non-covalently with and responding, e.g. by conformational change, to changes in the cellular level of oxygen (O2).
	GO:0036140	peptidyl-asparagine 3-dioxygenase activity	Catalysis of the reaction: peptidyl L-asparagine + 2-oxoglutarate + O2 = peptidyl 3-hydroxy-L-asparagine + succinate + CO2.
	GO:0036139	peptidyl-histidine dioxygenase activity	Catalysis of the reaction: peptidyl L-histidine + 2-oxoglutarate + O2 = peptidyl hydroxy-L-histidine + succinate + CO2.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0045746	negative regulation of Notch signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of the Notch signaling pathway.
	GO:0061428	negative regulation of transcription from RNA polymerase II promoter in response to hypoxia	Any process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0042265	peptidyl-asparagine hydroxylation	The hydroxylation of peptidyl-asparagine to form peptidyl-hydroxyasparagine.
	GO:0042264	peptidyl-aspartic acid hydroxylation	The hydroxylation of peptidyl-aspartic acid to form peptidyl-hydroxyaspartic acid.
	GO:0036138	peptidyl-histidine hydroxylation	The hydroxylation of peptidyl-histidine to form peptidyl-hydroxyhistidine.
	GO:0045663	positive regulation of myoblast differentiation	Any process that activates or increases the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
	GO:2001214	positive regulation of vasculogenesis	Any process that activates or increases the frequency, rate or extent of vasculogenesis.
	GO:0061418	regulation of transcription from RNA polymerase II promoter in response to hypoxia	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

Asymmetric Unit
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	Cis Peptide Bonds
		Tyr A:308 - Pro A:309	[ RasMol ]

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	2xum
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1h2k	FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH HIF-1 ALPHA FRAGMENT PEPTIDE
1h2l	FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH HIF-1 ALPHA FRAGMENT PEPTIDE
1h2m	FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH HIF-1 ALPHA FRAGMENT PEPTIDE
1h2n	FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH HIF-1 ALPHA FRAGMENT PEPTIDE
1iz3	DIMERIC STRUCTURE OF FIH (FACTOR INHIBITING HIF)
1mze	HUMAN FACTOR INHIBITING HIF (FIH1)
1mzf	HUMAN FACTOR INHIBITING HIF (FIH1) IN COMPLEX WITH 2-OXOGLUTARATE
1yci	FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH N-(CARBOXYCARBONYL)-D-PHENYLALANINE
2cgn	FACTOR INHIBITING HIF-1 ALPHA WITH SUCCINATE
2cgo	FACTOR INHIBITING HIF-1 ALPHA WITH FUMARATE
2w0x	FACTOR INHIBITING HIF-1 ALPHA WITH PYRIDINE 2,4 DICARBOXYLIC ACID
2wa3	FACTOR INHIBITING HIF-1 ALPHA WITH 2-(3- HYDROXYPHENYL)-2-OXOACETIC ACID
2wa4	FACTOR INHIBITING HIF-1 ALPHA WITH N,3- DIHYDROXYBENZAMIDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (1, 1)

Exons (8, 8)

Sequences/Alignments

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SCOP Domains (1, 1)

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Pfam Domains (0, 0)

Gene Ontology (32, 32)

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