4NHM - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF TPA1P FROM SACCHAROMYCES CEREVISIAE, TERMINATION AND POLYADENYLATION PROTEIN 1, IN COMPLEX WITH N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE (IOX3/UN9)

Authors :   J. S. Scotti, M. A. Mcdonough, C. J. Schofield

Date :   05 Nov 13 (Deposition) - 19 Nov 14 (Release) - 29 Apr 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   2-Oxoglutarate Oxygenase, Oxygen Sensing, Protein Synthesis Regulation, Double-Stranded Beta Helix, Jellyroll Fold, Prolyl Hydroxylase, Translation, Ribosome, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Horita, J. S. Scotti, C. Thinnes, Y. S. Mottaghi-Taromsari, A. Thalhammer, W. Ge, W. Aik, C. Loenarz, C. J. Schofield, M. A. Mcdonough
Structure Of The Ribosomal Oxygenase Ogfod1 Provides Insights Into The Regio- And Stereoselectivity Of Prolyl Hydroxylases.
Structure V. 23 639 2015
PubMed-ID: 25728928 | Reference-DOI: 10.1016/J.STR.2015.01.014

Molecule 1 - PKHD-TYPE HYDROXYLASE TPA1
	Chains	:	A
	EC Number	:	1.14.11.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	TPA1, YER049W
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	S288C
	Synonym	:	TERMINATION AND POLYADENYLATION PROTEIN 1

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MN	1	Ligand/Ion	MANGANESE (II) ION
3	UN9	1	Ligand/Ion	N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:148 , TYR A:150 , LEU A:156 , HIS A:159 , ASP A:161 , ILE A:171 , TYR A:173 , LEU A:189 , HIS A:227 , VAL A:229 , ARG A:238 , GLN A:242 , TRP A:244 , MN A:702 , GOL A:703 , HOH A:814 , HOH A:1325 , HOH A:1329	BINDING SITE FOR RESIDUE UN9 A 701
2	AC2	SOFTWARE	HIS A:159 , ASP A:161 , HIS A:227 , UN9 A:701 , HOH A:1325	BINDING SITE FOR RESIDUE MN A 702
3	AC3	SOFTWARE	ILE A:87 , LEU A:156 , UN9 A:701 , HOH A:960 , HOH A:1204 , HOH A:1329	BINDING SITE FOR RESIDUE GOL A 703
4	AC4	SOFTWARE	PHE A:519 , ASN A:520 , LEU A:523 , LYS A:524 , ILE A:529 , ILE A:530 , ASP A:531 , ASP A:631	BINDING SITE FOR RESIDUE GOL A 704

(no "SS Bond" information available for 4NHM)

Asymmetric/Biological Unit

No.	Residues
1	Gln A:51	-	Pro A:52
2	Phe A:284	-	Pro A:285
3	Ala A:401	-	Pro A:402
4	Ile A:407	-	Pro A:408

(no "SAP(SNP)/Variant" information available for 4NHM)

(no "PROSITE Motif" information available for 4NHM)

(no "Exon" information available for 4NHM)

Asymmetric/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:546
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhh..eeee...eeeee.................hhhhhhhhhhhhhhhhhhhhhhhh...........eeeeee....eeeee......eeeeeeee........hhhhh..eee..eee..ee.....eee......eeeee.......eee........eeeeeeeee....hhhhh....hhhhh......ee.hhhhhhhhhhhhh...hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhheeeee...hhhhhhhhhhhhhhhhhhh....hhhhh....ee......ee.eee.........hhhhhhhhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhheee.eeeeeeeee.....ee.......hhhhh....eeeeeeeeeeee..............eeee...eeeee...eeeeeeeee....eeee..........eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4nhm A  23 EDKIKGMFNPKIWDKTFQDGLKKEIEDSQPYNWGTIHELVNDDLLRAVRKEIETEIHFTKKETDIYRVNQSGDLANLSGLDWDDLSRLPNLFKLRQILYSKQYRDFFGYVTKAGKLSGSKTDMSINTYTKGCHLLTHDDVIGSRRISFILYLPDPDRKWKSHYGGGLRLFPSILPNVPHSDPSAKLVPQFNQIAFFKVLPGFSFHDVEEVKVDKHRLSIQGWYHIPQVGEEGYIPGELEDFEFPKDERNILSFHEVKHFEKMLKVKLSEAEFTYLSQYISPEHLSSKGIEKLQKQFVENSSLQIESFLNDDKSELLKKVIKQKELEQECPYHSKDVKAPWKTAIPPHKARYLYIDGKEYRNFQTEADILEALNNNDLPNFQFTKDAIKIISDASGNSRENNFDAELALIDLAVFHKSTIFKKYLALLTSLCPVSEQILIRRFRPGMDFTLATKCRFNELLKSNPDIIDAVLEGTLCLTPSAGWESGELGGYELYMMDSVLINDPPAWNTFNLVLRDESVLEFVKYVSWSAKSSRWDVKMKWDVKSC 635
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252      |281       291       301   ||  333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553      |589       599       609       619       629      
                                                                                                                                                                                                                                                                      259|                       305|                                                                                                                                                                                                                                     560|                                                
                                                                                                                                                                                                                                                                       279                        328                                                                                                                                                                                                                                      587

Legend:		→ Mismatch	(orange background)
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	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 4NHM)

(no "CATH Domain" information available for 4NHM)

(no "Pfam Domain" information available for 4NHM)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:401 - Pro A:402	[ RasMol ]
		Gln A:51 - Pro A:52	[ RasMol ]
		Ile A:407 - Pro A:408	[ RasMol ]
		Phe A:284 - Pro A:285	[ RasMol ]

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	4nhm
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	TPA1_YEAST \| P40032
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	1.14.11.-
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	TPA1_YEAST \| P40032
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UniProtKB/Swiss-Prot
	TPA1_YEAST \| P40032	:	3kt1 3kt4 3kt7 3mgu 4nhk 4nhl

Description

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Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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Exons (0, 0)

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