4UOY: YgjG

Name: PDB 4UOY: Crystal structure of YgjG in complex with Pyridoxal-5'-phosphate
Published: 2014-12-10
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal structure of YgjG in complex with Pyridoxal-5'-phosphate. Determined by X-ray diffraction at 2.31 Å resolution. Released 10 Dec 2014.

Method: X-ray diffraction
Resolution: 2.31 Å
Organism: ESCHERICHIA COLI
Chains: 4
Atoms: 14,158
Mol. weight: 204.36 kDa
Ligands: PLP
Released: 10 Dec 2014

Explore 4UOY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4UOY contains 100 α-helices and 76 β-strands across 4 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: 23 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	10-22	13
α-helix	28-41	14
α-helix	42-46	5
α-helix	48-55	8
α-helix	60-64	5
β-strand	66	1	1
β-strand	67-72	6	2
β-strand	75-78	4	2
β-strand	83-86	4	2
α-helix	89-92	4
α-helix	101-113	13
β-strand	122	1	3
α-helix	124-136	13
β-strand	141-147	7	4
α-helix	150-165	16
β-strand	172-176	5	4
α-helix	185-188	4
α-helix	194-197	4
α-helix	198-200	3
β-strand	207-210	4	4
α-helix	215-227	13
β-strand	232-237	6	4
β-strand	241	1	5
β-strand	247	1	5
α-helix	248-250	3
α-helix	253-264	12
β-strand	267-271	5	4
α-helix	285-288	4
β-strand	295-298	4	4
α-helix	300-303	4
β-strand	310-315	6	4
α-helix	316-319	4
α-helix	320-322	3
α-helix	337-352	16
α-helix	355-376	22
β-strand	381-387	7	6
β-strand	390-395	6	6
α-helix	398-410	13
β-strand	413-414	2	2
β-strand	416-418	3	6
β-strand	421-427	7	6
α-helix	435-459	25

Chain B: 25 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	10-22	13
α-helix	28-41	14
α-helix	42-46	5
α-helix	48-55	8
α-helix	60-64	5
β-strand	66	1	3
β-strand	67-72	6	7
β-strand	75-78	4	7
β-strand	83-86	4	7
α-helix	89-92	4
α-helix	101-111	11
β-strand	122	1	1
α-helix	123	1
α-helix	124-136	13
β-strand	141-147	7	8
α-helix	150-165	16
α-helix	166-168	3
β-strand	172-176	5	8
α-helix	187-190	4
α-helix	194-197	4
α-helix	198-200	3
β-strand	207-210	4	8
α-helix	215-228	14
β-strand	232-237	6	8
β-strand	241	1	9
β-strand	247	1	9
α-helix	248-250	3
α-helix	253-264	12
β-strand	267-271	5	8
α-helix	285-287	3
β-strand	295-298	4	8
α-helix	300-303	4
β-strand	310-315	6	8
α-helix	316-319	4
α-helix	320-322	3
α-helix	337-352	16
α-helix	355-376	22
β-strand	381-387	7	10
β-strand	390-395	6	10
α-helix	398-410	13
β-strand	413-414	2	7
β-strand	416-418	3	10
β-strand	421-427	7	10
α-helix	435-458	24

Chain C: 26 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	10-22	13
α-helix	28-41	14
α-helix	42-46	5
α-helix	48-56	9
α-helix	60-64	5
β-strand	66	1	11
β-strand	67-70	4	12
β-strand	75-78	4	12
β-strand	83-86	4	12
α-helix	89-92	4
α-helix	101-113	13
β-strand	122	1	13
α-helix	123	1
α-helix	124-136	13
β-strand	141-147	7	14
α-helix	150-165	16
α-helix	166-168	3
β-strand	172-176	5	14
α-helix	185-190	6
α-helix	194-197	4
α-helix	198-200	3
β-strand	207-210	4	14
α-helix	215-227	13
β-strand	232-237	6	14
β-strand	241	1	15
β-strand	247	1	15
α-helix	248-250	3
α-helix	253-264	12
α-helix	266	1
β-strand	267-271	5	14
α-helix	285-289	5
β-strand	295-298	4	14
α-helix	300-303	4
β-strand	310-315	6	14
α-helix	316-319	4
α-helix	320-322	3
α-helix	337-352	16
α-helix	355-376	22
β-strand	381-387	7	16
β-strand	390-395	6	16
α-helix	398-410	13
β-strand	413-414	2	12
β-strand	416-418	3	16
β-strand	421-427	7	16
α-helix	435-458	24

Chain D: 26 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	10-22	13
α-helix	28-41	14
α-helix	42-46	5
α-helix	48-56	9
α-helix	60-62	3
β-strand	66	1	13
β-strand	67-70	4	17
β-strand	75-78	4	17
β-strand	83-86	4	17
α-helix	89-91	3
α-helix	101-113	13
β-strand	122	1	11
α-helix	123	1
α-helix	124-136	13
β-strand	141-147	7	18
α-helix	150-165	16
α-helix	166-168	3
β-strand	172-176	5	18
α-helix	187-189	3
α-helix	194-197	4
α-helix	198-200	3
β-strand	207-210	4	18
α-helix	215-227	13
β-strand	232-237	6	18
β-strand	241	1	19
β-strand	247	1	19
α-helix	248-250	3
α-helix	253-264	12
α-helix	266	1
β-strand	267-271	5	18
α-helix	285-288	4
β-strand	295-298	4	18
α-helix	300-303	4
β-strand	310-315	6	18
α-helix	316-319	4
α-helix	320-322	3
α-helix	337-352	16
α-helix	355-376	22
β-strand	381-387	7	20
β-strand	390-395	6	20
α-helix	398-410	13
β-strand	413-414	2	17
β-strand	416-417	2	20
β-strand	424-427	4	20
α-helix	435-458	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Putrescine aminotransferase	A, B, C, D	protein	467	ESCHERICHIA COLI	P42588 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>4UOY_1 PUTRESCINE AMINOTRANSFERASE (chains A, B, C, D)
MNRLPSSASALACSAHALNLIEKRTLDHEEMKALNREVIEYFKEHVNPGFLEYRKSVTAG
GDYGAVEWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQE
LLDPLRAMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAF
HGKSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPI
QGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAK
ALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAE
QKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLN
NAKTIRIEPPLTLTIEQCELVIKAARKALAAMRVSVEEALEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
PLP	Pyridoxal-5'-phosphate	C8 H10 N O6 P	4

Water and common crystallization additives (GOL, FMT) are not listed.

Primary citation

Structure of Putrescine Aminotransferase from Escherichia Coli Provides Insights Into the Substrate Specificity Among Class III Aminotransferases. Cha, H.J., Jeong, J., Rojviriya, C. et al. PLoS One (2014) 9:13212. DOI 10.1371/JOURNAL.PONE.0113212 · PubMed

Other PDB entries of the same protein (UniProt P42588 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8CPL 1.6 Å, YZw2 a scaffold for cryo-EM of small proteins of interest
4UOX 2.08 Å, Crystal structure of YgjG in complex with Pyridoxal-5'-phosphate and putrescine
8R2P 2.22 Å, YZwIdeal x16 a scaffold for cryo-EM of small proteins of interest crystallizing in space…
5H7D 2.57 Å, Crystal structure of the YgjG-protein A-Zpa963-calmodulin complex
5X3F 3.38 Å, Crystal structure of the YgjG-Protein A-Zpa963-PKA catalytic domain

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