1Y1H - JenaLib

Title :   HUMAN FORMYLGLYCINE GENERATING ENZYME, OXIDISED CYS REFINED AS HYDROPEROXIDE

Authors :   M. G. Rudolph, A. Dickmanns, R. Ficner

Date :   18 Nov 04 (Deposition) - 31 May 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.67

Chains :   Asym./Biol. Unit : X

Keywords :   Formylglycine, Multiple Sulfatase Deficiency, Cysteine Sulfenic Acid, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Dierks, A. Dickmanns, A. Preusser-Kunze, B. Schmidt, M. Mariappan K. Von Figura, R. Ficner, M. G. Rudolph
Molecular Basis For Multiple Sulfatase Deficiency And Mechanism For Formylglycine Generation Of The Human Formylglycine-Generating Enzyme.
Cell(Cambridge, Mass. ) V. 121 541 2005
PubMed-ID: 15907468 | Reference-DOI: 10.1016/J.CELL.2005.03.001

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (3, 3)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (13, 13)

Asymmetric/Biological Unit (13, 13)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_016053	S	155	P	SUMF1_HUMAN	Disease (MSD)	137852850	X	S	155	P
02	UniProt	VAR_019051	A	177	P	SUMF1_HUMAN	Disease (MSD)	---	X	A	177	P
03	UniProt	VAR_042602	W	179	S	SUMF1_HUMAN	Disease (MSD)	757323641	X	W	179	S
04	UniProt	VAR_016054	C	218	Y	SUMF1_HUMAN	Disease (MSD)	137852854	X	C	218	Y
05	UniProt	VAR_019052	R	224	W	SUMF1_HUMAN	Disease (MSD)	759888604	X	R	224	W
06	UniProt	VAR_019053	N	259	I	SUMF1_HUMAN	Disease (MSD)	764215221	X	N	259	I
07	UniProt	VAR_019054	P	266	L	SUMF1_HUMAN	Disease (MSD)	763243827	X	P	266	L
08	UniProt	VAR_016055	A	279	V	SUMF1_HUMAN	Disease (MSD)	137852849	X	A	279	V
09	UniProt	VAR_016056	C	336	R	SUMF1_HUMAN	Disease (MSD)	137852848	X	C	336	R
10	UniProt	VAR_016057	R	345	C	SUMF1_HUMAN	Disease (MSD)	137852852	X	R	345	C
11	UniProt	VAR_016058	A	348	P	SUMF1_HUMAN	Disease (MSD)	137852853	X	A	348	P
12	UniProt	VAR_016059	R	349	Q	SUMF1_HUMAN	Disease (MSD)	137852847	X	R	349	Q
13	UniProt	VAR_016060	R	349	W	SUMF1_HUMAN	Disease (MSD)	137852846	X	R	349	W

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

PROSITE Motifs (0, 0)

Exons (9, 9)

Asymmetric/Biological Unit (9, 9)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000272902	1a	ENSE00001901311	chr3:4508965-4508660	306	SUMF1_HUMAN	1-90	90	1	X:86-90	5
1.2	ENST00000272902	2	ENSE00000965223	chr3:4494733-4494560	174	SUMF1_HUMAN	91-148	58	1	X:91-148	58
1.3	ENST00000272902	3	ENSE00001173781	chr3:4491024-4490950	75	SUMF1_HUMAN	149-173	25	1	X:149-162	14
1.4	ENST00000272902	4	ENSE00001173775	chr3:4461830-4461748	83	SUMF1_HUMAN	174-201	28	1	X:175-201	27
1.5	ENST00000272902	5	ENSE00001173770	chr3:4459816-4459694	123	SUMF1_HUMAN	201-242	42	1	X:201-242	42
1.6	ENST00000272902	6	ENSE00001173766	chr3:4458926-4458812	115	SUMF1_HUMAN	242-280	39	1	X:242-280	39
1.7	ENST00000272902	7	ENSE00001173758	chr3:4452662-4452549	114	SUMF1_HUMAN	281-318	38	1	X:281-318	38
1.8	ENST00000272902	8	ENSE00001173755	chr3:4418073-4418014	60	SUMF1_HUMAN	319-338	20	1	X:319-338	20
1.9d	ENST00000272902	9d	ENSE00001072608	chr3:4403938-4402830	1109	SUMF1_HUMAN	339-374	36	1	X:339-372	34

Sequences/Alignments

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
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain X from PDB  Type:PROTEIN  Length:275
 aligned with SUMF1_HUMAN | Q8NBK3 from UniProtKB/Swiss-Prot  Length:374

    Alignment length:287
                                    95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       
          SUMF1_HUMAN    86 LAHSKMVPIPAGVFTMGTDDPQIKQDGEAPARRVTIDAFYMDAYEVSNTEFEKFVNSTGYLTEAEKFGDSFVFEGMLSEQVKTNIQQAVAAAPWWLPVKGANWRHPEGPDSTILHRPDHPVLHVSWNDAVAYCTWAGKRLPTEAEWEYSCRGGLHNRLFPWGNKLQPKGQHYANIWQGEFPVTNTGEDGFQGTAPVDAFPPNGYGLYNIVGNAWEWTSDWWTVHHSVEETLNPKGPPSGKDRVKKGGSYMCHRSYCYRYRCAARSQNTPDSSASNLGFRCAADRLPT 372
               SCOP domains d1y1hx_ X: automated matches                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1y1hX00 X:86-372 paralog of FGE (formylglycine-generating enzyme)                                                                                                                                                                                                                               CATH domains
               Pfam domains -FGE-sulfatase-1y1hX01 X:87-367                                                                                                                                                                                                                                                           ----- Pfam domains
         Sec.struct. author .....eeee..eeeee......hhhhh....eeeee..eeee....hhhhhhhhhhhhh..hhhhhhheeeee.hhh------------.....eeeee.........................hhhhhhhhhhhh.....hhhhhhhhhhh.............hhhhh.......ee...ee.............................eeeeeee.........ee..........eeee...................eee........ee...ee..... Sec.struct. author
             SAPs(SNPs) (1) ---------------------------------------------------------------------P---------------------P-S--------------------------------------Y-----W----------------------------------I------L------------V--------------------------------------------------------R--------C--PQ----------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------W----------------------- SAPs(SNPs) (2)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1a Exon 1.2  PDB: X:91-148 UniProt: 91-148                   Exon 1.3  PDB: X:149-162 Exon 1.4  PDB: X:175-201    ----------------------------------------Exon 1.6  PDB: X:242-280               Exon 1.7  PDB: X:281-318              Exon 1.8            Exon 1.9d  PDB: X:339-372          Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------Exon 1.5  PDB: X:201-242 UniProt: 201-242 ---------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1y1h X  86 LAHSKMVPIPAGVFTMGTDDPQIKQDGEAPARRVTIDAFYMDAYEVSNTEFEKFVNSTGYLTEAEKFGDSFVFEGML------------AAAPWWLPVKGANWRHPEGPDSTILHRPDHPVLHVSWNDAVAYCTWAGKRLPTEAEWEYSCRGGLHNRLFPWGNKLQPKGQHYANIWQGEFPVTNTGEDGFQGTAPVDAFPPNGYGLYNIVGNAWEWTSDWWTVHHSVEETLNPKGPPSGKDRVKKGGSYMCHRSYCYRYRCAARSQNTPDSSASNLGFRCAADRLPT 372
                                    95       105       115       125       135       145       155      |  -       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       
                                                                                                      162          175

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ 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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain X (SUMF1_HUMAN | Q8NBK3)

molecular function
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0006687	glycosphingolipid metabolic process	The chemical reactions and pathways involving glycosphingolipids, any compound with residues of sphingoid and at least one monosaccharide.
	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:0043687	post-translational protein modification	The process of covalently altering one or more amino acids in a protein after the protein has been completely translated and released from the ribosome.
cellular component
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005788	endoplasmic reticulum lumen	The volume enclosed by the membranes of the endoplasmic reticulum.

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