1UM2: Endonuclease pi-scei

Crystal Structure of the Vma1-Derived Endonuclease with the Ligated Extein Segment. Determined by X-ray diffraction at 2.9 Å resolution. Released 22 Sept 2004.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 6,865
Mol. weight: 106.39 kDa
Released: 22 Sept 2004

Explore 1UM2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1UM2 contains 27 α-helices and 71 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 13 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	285	1	1
β-strand	290	1	2
β-strand	291	1	3
β-strand	293	1	4
β-strand	300	1	2
β-strand	309-311	3	4
β-strand	317-319	3	4
β-strand	325-335	11	1
β-strand	355-359	5	1
β-strand	363-369	7	5
β-strand	372-374	3	6
β-strand	377-378	2	7
β-strand	383-384	2	7
β-strand	387-396	10	6
β-strand	402-411	10	6
β-strand	414	1	7
α-helix	415-417	3
α-helix	420-432	13
β-strand	437-443	7	5
α-helix	444-449	6
α-helix	452-456	5
β-strand	459	1	5
β-strand	460-462	3	8
α-helix	471-476	6
α-helix	487-499	13
β-strand	508	1	9
α-helix	518-529	12
β-strand	535	1	10
β-strand	547	1	10
β-strand	548	1	9
α-helix	568-575	8
α-helix	588-590	3
α-helix	595-609	15
β-strand	611-613	3	11
β-strand	615	1	12
β-strand	617	1	12
β-strand	619-624	6	11
α-helix	627-640	14
β-strand	643-649	7	11
β-strand	663-669	7	11
α-helix	672-678	7
α-helix	689-691	3
β-strand	700-702	3	8
β-strand	704-715	12	1
β-strand	726-728	3	13
β-strand	729	1	3
β-strand	733	1	8
β-strand	734-736	3	13

Chain B: 14 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	285	1	14
β-strand	290-292	3	15
β-strand	293	1	16
β-strand	298-300	3	15
β-strand	309-311	3	16
β-strand	317-319	3	16
β-strand	320	1	17
β-strand	325-328	4	14
β-strand	330-335	6	14
β-strand	355-359	5	14
β-strand	363-369	7	18
β-strand	372-379	8	19
β-strand	382-392	11	19
β-strand	406-409	4	19
β-strand	414	1	19
α-helix	415-417	3
α-helix	421-424	4
α-helix	426-430	5
β-strand	437-443	7	18
α-helix	452-457	6
β-strand	459-462	4	18
α-helix	471-475	5
α-helix	487-501	15
β-strand	502	1	20
β-strand	509-512	4	20
α-helix	516-526	11
β-strand	535	1	20
β-strand	544-547	4	20
α-helix	568-575	8
β-strand	579-580	2	21
β-strand	583-584	2	21
α-helix	588-592	5
α-helix	595-609	15
β-strand	610-613	4	22
β-strand	619-624	6	22
α-helix	627-640	14
β-strand	643-649	7	22
β-strand	663-669	7	22
α-helix	672-678	7
α-helix	689-691	3
α-helix	698-699	2
β-strand	700-702	3	18
β-strand	704-708	5	14
β-strand	712-715	4	14
β-strand	719	1	17
β-strand	726-728	3	18
β-strand	729	1	15
β-strand	733-736	4	18

Chain D: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	282	1	23
β-strand	740	1	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Endonuclease pi-scei	A, B	protein	454	Saccharomyces cerevisiae	P17255 (AlphaFold model)
21-mer from Vacuolar ATP synthase catalytic subunit A	C, D	protein	21	Saccharomyces cerevisiae	P17255 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1UM2_1 ENDONUCLEASE PI-SCEI (chains A, B)
SFAKGTNVLMADGSIECIENIEVGNKVMGKDGRPREVIKLPRGRETMYSVVQKSQHRAHK
SDSSREVPELLKFTCNATNELVVRTPRSVRRLSRTIKGVEYFEVITFEMGQKKAPDGRIV
ELVKEVSKSYPISEGPERANELVESYRKASNKAYFEWTIEARDLSLLGSHVRKATYQTYA
PILYENDHFFDYMQKSKFHLTIEGPKVLAYLLGLWIGDGLSDRATFSVDSRDTSLMERVT
EYAEKLNLCAEYKDRKEPQVAKTVNLYSKVVRGNGIRNNLNTENPLWDAIVGLGFLKDGV
KNIPSFLSTDNIGTRETFLAGLIDSDGYVTDEHGIKATIKTIHTSVRDGLVSLARSLGLV
VSVNAEPAKVDMNGTKHKISYAIYMSGGDVLLNVLSKCAGSKKFRPAPAAAFARECRGFY
FELQELKEDDYYGITLSDDSDHQFLLANQVVVHN

Sequence of entity 2 (C, D), FASTA

>1UM2_2 21-mer from Vacuolar ATP synthase catalytic subunit A (chains C, D)
MSNSDAIIYVGSGERGNEMAE

Primary citation

Protein splicing of yeast VMA1-derived endonuclease via thiazolidine intermediates. Mizutani, R., Anraku, Y., Satow, Y. J Synchrotron Radiat (2004) 11:109-112. DOI 10.1107/s0909049503023495 · PubMed

Other PDB entries of the same protein (UniProt P17255 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1GPP 1.35 Å, Crystal structure of the S.cerevisiae Homing Endonuclease PI-SceI Domain I
1DFA 2.0 Å, Crystal structure of pi-scei in C2 space group
1EF0 2.1 Å, Crystal structure of pi-scei miniprecursor
1JVA 2.1 Å, Crystal structure of the VMA1-derived endonuclease bearing the N and C extein propeptides
1VDE 2.4 Å, Pi-scei, a homing endonuclease with protein splicing activity
9COP 2.7 Å, Yeast RAVE bound to V-ATPase V1 complex
1LWT 3.2 Å, Crystal structure of the intein homing endonuclease PI-SceI bound to its substrate DNA…
7TMO 3.3 Å, V1 complex lacking subunit C from Saccharomyces cerevisiae, State 1
7TMP 3.3 Å, V1 complex lacking subunit C from Saccharomyces cerevisiae, State 2
7TMQ 3.3 Å, V1 complex lacking subunit C from Saccharomyces cerevisiae, State 3
1LWS 3.5 Å, Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition…
7TMM 3.5 Å, Complete V1 Complex from Saccharomyces cerevisiae

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