5F13 - JenaLib

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Title :   STRUCTURE OF MN BOUND DUF89 FROM SACCHAROMYCES CEREVISIAE

Authors :   B. Nocek, T. Skarina, A. Joachimiak, A. Savchenko, A. Yakunin

Date :   30 Nov 15 (Deposition) - 30 Mar 16 (Release) - 03 Aug 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.39

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

Keywords :   Duf89, Metal-Dependent Phosphatases, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Huang, A. Khusnutdinova, B. Nocek, G. Brown, X. Xu, H. Cui, P. Petit, R. Flick, R. Zallot, K. Balmant, M. J. Ziemak, J. Shanklin, V. De Crecy-Lagard, O. Fiehn, J. F. Gregory, A. Joachimiak, A. Savchenko, A. F. Yakunin, A. D. Hanson
A Family Of Metal-Dependent Phosphatases Implicated In Metabolite Damage-Control.
Nat. Chem. Biol. V. 12 621 2016
PubMed-ID: 27322068 | Reference-DOI: 10.1038/NCHEMBIO.2108

Molecule 1 - PROTEIN-GLUTAMATE O-METHYLTRANSFERASE
	Chains	:	A, B, C
	EC Number	:	2.1.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
	Expression System Taxid	:	866768
	Gene	:	YMR027W, YM9711.17
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
	Organism Taxid	:	559292
	Strain	:	ATCC 204508 / S288C

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 13)

No.	Name	Count	Type	Full Name
1	CL	3	Ligand/Ion	CHLORIDE ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	MN	3	Ligand/Ion	MANGANESE (II) ION
4	PO4	6	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:254 , ASN A:255 , ASP A:292 , PO4 A:502 , HOH A:632 , HOH A:636	binding site for residue MN A 501
02	AC2	SOFTWARE	ASP A:254 , ASN A:255 , ASP A:384 , LEU A:385 , LYS A:423 , MN A:501 , PO4 A:503 , HOH A:627 , HOH A:632	binding site for residue PO4 A 502
03	AC3	SOFTWARE	GLU A:110 , ASP A:384 , LEU A:385 , ARG A:388 , PO4 A:502 , HOH A:611 , HOH A:615 , HOH A:649	binding site for residue PO4 A 503
04	AC4	SOFTWARE	HIS A:38 , ARG A:135	binding site for residue CL A 504
05	AC5	SOFTWARE	HIS A:282 , GLU A:344 , ASP A:345 , TRP A:348	binding site for residue CL A 505
06	AC6	SOFTWARE	ASP B:254 , ASN B:255 , ASP B:292 , PO4 B:502 , HOH B:608 , HOH B:628	binding site for residue MN B 501
07	AC7	SOFTWARE	ASP B:254 , ASN B:255 , ASP B:384 , LEU B:385 , MN B:501 , PO4 B:503 , HOH B:603 , HOH B:608 , HOH B:628	binding site for residue PO4 B 502
08	AC8	SOFTWARE	GLU B:110 , ASP B:384 , LEU B:385 , ARG B:388 , PO4 B:502 , HOH B:601	binding site for residue PO4 B 503
09	AC9	SOFTWARE	HIS B:38	binding site for residue CL B 504
10	AD1	SOFTWARE	ARG B:248 , ARG B:343 , ASP B:372 , ARG C:248 , ARG C:343 , ASP C:372	binding site for residue EDO B 505
11	AD2	SOFTWARE	ASP C:254 , ASN C:255 , ASP C:292 , PO4 C:502 , HOH C:608 , HOH C:609	binding site for residue MN C 501
12	AD3	SOFTWARE	ASP C:254 , ASN C:255 , ASP C:384 , LEU C:385 , LYS C:423 , MN C:501 , PO4 C:503 , HOH C:608 , HOH C:609	binding site for residue PO4 C 502
13	AD4	SOFTWARE	GLU C:110 , ASP C:384 , LEU C:385 , ARG C:388 , PO4 C:502	binding site for residue PO4 C 503

Asymmetric Unit

No.	Residues
1	A:125	-	A:125
2	B:125	-	C:125

(no "Cis Peptide Bond" information available for 5F13)

(no "SAP(SNP)/Variant" information available for 5F13)

(no "PROSITE Motif" information available for 5F13)

(no "Exon" information available for 5F13)

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:445
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh..hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhheeeehhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhhhhhh....eeeeee...........hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh..hhhhh.......hhhhhhhhhh...eeeeehhhhhhhhh.........hhhhhhhhhhh....eeeeee...........hhhhhhhhhhh.....hhhhhhhh...eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f13 A   3 IPGRFMTIDKGTFGEYTASTRWPIIIQNAIDDLSKHQETEKSNGTKFEQGEVIKKELKEFRQEIIDRVPLRPFTEEEIKIANVPLSFNEYLKKHPEVNWGAVEWLFSEVYLYRRVNVLFQRQCEWAKFDIFNRLKQSTFESSFYGVVELALRYENLLPQLREMKNEIDDILKVLFKEFIEISLWGSIQGAKARAASESKIVVNDTEKAWEVLTKARADANSREIRVDFVLDNSGFELYADLMLAAFLLQSGLATKCIFHAKDIPYMVSDVMLKDFDILVHDLRDREFFPSGEPSTKESRALDLFAGEMEKFVSSGKIEFREDSFWTTELDYWNLDANETKYHGSILHKDLQKSNLVIFKGDLNYRKLTGDRKWPRTTKWETAIGPLATNGITSLSLRTCKADVQVALPEGLDAKLSQEWEKENPGRGSWWCCSGKWAVICFCSGI 468
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162   ||  176       186    || 213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463     
                                                                                                                                                                                             166|                 191|                                                                                                                                                                                                                                                                   
                                                                                                                                                                                              171                  209

Chain B from PDB  Type:PROTEIN  Length:449
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhheeeehhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh..hhhhh.......hhhhhhhhhh...eeeeehhhhhhhhh.........hhhhhhhhhhh....eeeeee...........hhhhhhhhhhh.....hhhhhhhh...eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f13 B   3 IPGRFMTIDKGTFGEYTASTRWPIIIQNAIDDLSKHQETEKSNGTKFEQGEVIKKELKEFRQEIIDRVPLRPFTEEEIKIANVPLSFNEYLKKHPEVNWGAVEWLFSEVYLYRRVNVLFQRQCEWAKFDIFNRLKQSTFESSFYGVVELALRYENLLPQLREMKQNPGNEIDDILKVLFKEFIEISLWGNDIKSIQGAKARAASESKIVVNDTEKAWEVLTKARADEIRVDFVLDNSGFELYADLMLAAFLLQSGLATKCIFHAKDIPYMVSDVMLKDFDILVHDLRDREFFPSGEPSTKESRALDLFAGEMEKFVSSGKIEFREDSFWTTELDYWNLDANETKYHGSILHKDLQKSNLVIFKGDLNYRKLTGDRKWPRTTKWETAIGPLATNGITSLSLRTCKADVQVALPEGLDAKLSQEWEKENPGRGSWWCCSGKWAVICFCSGI 468
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192|      215       225       235     ||249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459         
                                                                                                                                                                                                                       192|                                241|                                                                                                                                                                                                                              
                                                                                                                                                                                                                        206                                 246

Chain C from PDB  Type:PROTEIN  Length:444
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh..hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhheeeehhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh....eeeeee...........hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh..hhhhh.......hhhhhhhhhhh..eeeeehhhhhhhhhh........hhhhhhhhhhh....eeeeee...........hhhhhhhhhhh.....hhhhhhhh...eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5f13 C   3 IPGRFMTIDKGTFGEYTASTRWPIIIQNAIDDLSKHQETEGTKFEQGEVIKKELKEFRQEIIDRVPLRPFTEEEIKIANVPLSFNEYLKKHPEVNWGAVEWLFSEVYLYRRVNVLFQRQCEWAKFDIFNRLKQSTFESSFYGVVELALRYENLLPQLREMKQNDDILKVLFKEFIEISLWGTLEDIKSIQGAKARAASESKIVVNDTEKAWEVLTKARADREIRVDFVLDNSGFELYADLMLAAFLLQSGLATKCIFHAKDIPYMVSDVMLKDFDILVHDLRDREFFPSGEPSTKESRALDLFAGEMEKFVSSGKIEFREDSFWTTELDYWNLDANETKYHGSILHKDLQKSNLVIFKGDLNYRKLTGDRKWPRTTKWETAIGPLATNGITSLSLRTCKADVQVALPEGLDAKLSQEWEKENPGRGSWWCCSGKWAVICFCSGI 468
                                    12        22        32        42|       55        65        75        85        95       105       115       125       135       145       155       165  ||   180       190||     211       221       231       241|      254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464    
                                                                  42|                                                                                                                       168|              191|                                   241|                                                                                                                                                                                                                               
                                                                   46                                                                                                                        174               203                                    245

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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 5F13)

(no "CATH Domain" information available for 5F13)

(no "Pfam Domain" information available for 5F13)

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	5f13
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 13)

Sites (13, 13)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Gene Ontology (8, 8)

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