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234,785 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Enzyme Classification Number = 4.3.1.12

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Search Summary

This query matches 17 Structures.

Refinements

Structure Determination Methodology

experimental (17)

Scientific Name of Source Organism

	Streptomyces pristinaespiralis (8)
	Synechocystis sp. PCC 6803 substr. Kazusa (4)
	Nostoc sp. PCC 7120 = FACHB-418 (3)
	Pseudomonas putida (2)

Taxonomy

Bacteria (17)

Experimental Method

X-RAY DIFFRACTION (17)

Polymer Entity Type

Protein (17)

Refinement Resolution (Å)

	1.0 - 1.5 (3)
	1.5 - 2.0 (7)
	2.0 - 2.5 (5)
	2.5 - 3.0 (2)

Release Date

	2000 - 2004 (2)
	2015 - 2019 (8)
	2020 - 2024 (7)

Enzyme Classification Name

	Lyases (17)
	Hydrolases (7)

Symmetry Type

	Cyclic (10)
	Dihedral (4)
	Asymmetric (3)

SCOP Classification

Alpha and beta proteins (a/b) (6)

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1 to 17 of 17 Structures

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1U7H \| pdb_00001u7h	Download File View File

Structure and a Proposed Mechanism for Ornithine Cyclodeaminase from Pseudomonas putida

Alam, S., Goodman, J.L., Wang, S., Ruzicka, F.J., Frey, P.A., Wedekind, J.E.

(2004) Biochemistry 43: 13883-13891

Released	2004-11-09
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Pseudomonas putida
Macromolecule	ornithine cyclodeaminase (protein)
Unique Ligands	MPD, NA, NAD

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1X7D \| pdb_00001x7d	Download File View File

Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed with NAD and ornithine to 1.6 Angstroms

Alam, S., Goodman, J.L., Wang, S., Ruzicka, F.J., Frey, P.A., Wedekind, J.E.

(2004) Biochemistry 43: 13883-13891

Released	2004-11-09
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Pseudomonas putida
Macromolecule	ornithine cyclodeaminase (protein)
Unique Ligands	MES, MPD, NA, NAD, ORN

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5GZI \| pdb_00005gzi	Download File View File

Cyclodeaminase_PA

Ying, H., Chen, K.

To be published

Released	2018-01-17
Method	X-RAY DIFFRACTION 2.17 Å
Organisms	Streptomyces pristinaespiralis
Macromolecule	Lysine cyclodeaminase (protein)
Unique Ligands	NAD, YCP

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5GZJ \| pdb_00005gzj	Download File View File

Cyclodeaminase_PA

Ying, H., Chen, K.

To be published

Released	2018-01-17
Method	X-RAY DIFFRACTION 1.87 Å
Organisms	Streptomyces pristinaespiralis
Macromolecule	Lysine cyclodeaminase (protein)
Unique Ligands	NAD

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5GZL \| pdb_00005gzl	Download File View File

Cyclodeaminase_PA

Ying, H., Chen, K.

To be published

Released	2018-01-17
Method	X-RAY DIFFRACTION 2 Å
Organisms	Streptomyces pristinaespiralis
Macromolecule	Lysine cyclodeaminase (protein)
Unique Ligands	LYS, NAD

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5GZM \| pdb_00005gzm	Download File View File

Cyclodeaminase_PA

Ying, H., Chen, K.

To be published

Released	2018-01-17
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Streptomyces pristinaespiralis
Macromolecule	Lysine cyclodeaminase (protein)
Unique Ligands	NAD, YCP

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5YU0 \| pdb_00005yu0	Download File View File

Structural basis for recognition of L-lysine, L-ornithine, and L-2,4-diamino butyric acid by lysine cyclodeaminase

Min, K.J., Yoon, H.J., Matsuura, A., Kim, Y.H., Lee, H.H.

(2018) Mol Cells 41: 331-341

Released	2018-05-02
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Streptomyces pristinaespiralis
Macromolecule	Lysine cyclodeaminase (protein)
Unique Ligands	NA, NAD

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5YU1 \| pdb_00005yu1	Download File View File

Structural basis for recognition of L-lysine, L-ornithine, and L-2,4-diamino butyric acid by lysine cyclodeaminase

Min, K.J., Yoon, H.J., Matsuura, A., Kim, Y.H., Lee, H.H.

(2018) Mol Cells 41: 331-341

Released	2018-05-02
Method	X-RAY DIFFRACTION 1.923 Å
Organisms	Streptomyces pristinaespiralis
Macromolecule	Lysine cyclodeaminase (protein)
Unique Ligands	NA, NAD, YCP

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5YU3 \| pdb_00005yu3	Download File View File

Structural basis for recognition of L-lysine, L-ornithine, and L-2,4-diamino butyric acid by lysine cyclodeaminase

Min, K.J., Yoon, H.J., Matsuura, A., Kim, Y.H., Lee, H.H.

(2018) Mol Cells 41: 331-341

Released	2018-05-02
Method	X-RAY DIFFRACTION 1.79 Å
Organisms	Streptomyces pristinaespiralis
Macromolecule	Lysine cyclodeaminase (protein)
Unique Ligands	NA, NAD, PRO

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5YU4 \| pdb_00005yu4	Download File View File

Structural basis for recognition of L-lysine, L-ornithine, and L-2,4-diamino butyric acid by lysine cyclodeaminase

Min, K.J., Yoon, H.J., Matsuura, A., Kim, Y.H., Lee, H.H.

(2018) Mol Cells 41: 331-341

Released	2018-05-02
Method	X-RAY DIFFRACTION 2.144 Å
Organisms	Streptomyces pristinaespiralis
Macromolecule	Lysine cyclodeaminase (protein)
Unique Ligands	DAB, NA, NAD

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6JUY \| pdb_00006juy	Download File View File

Crystal Structure of ArgZ, apo structure, an Arginine Dihydrolase from the Ornithine-Ammonia Cycle in Cyanobacteria

Zhuang, N., Li, L., Wu, X., Zhang, Y.

(2020) J Biological Chem 295: 2113-2124

Released	2020-01-15
Method	X-RAY DIFFRACTION 2.97 Å
Organisms	Synechocystis sp. PCC 6803 substr. Kazusa
Macromolecule	Sll1336 protein (protein)

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6JUZ \| pdb_00006juz	Download File View File

Crystal Structure of N-terminal domain of ArgZ(N71S) covalently bond to a reaction intermediate

Zhuang, N., Li, L., Wu, X., Zhuang, Y.

(2020) J Biological Chem 295: 2113-2124

Released	2020-01-15
Method	X-RAY DIFFRACTION 1.21 Å
Organisms	Synechocystis sp. PCC 6803 substr. Kazusa
Macromolecule	Sll1336 protein (protein)
Unique Ligands	ARG, EDO

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6JV0 \| pdb_00006jv0	Download File View File

Crystal Structure of N-terminal domain of ArgZ, bound to Product, an arginine dihydrolase from the Ornithine-Ammonia Cycle in Cyanobacteria

Zhuang, N., Li, L., Wu, X., Zhang, Y.

(2020) J Biological Chem 295: 2113-2124

Released	2020-01-15
Method	X-RAY DIFFRACTION 1.14 Å
Organisms	Synechocystis sp. PCC 6803 substr. Kazusa
Macromolecule	Sll1336 protein (protein)
Unique Ligands	EDO, ORN

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6JV1 \| pdb_00006jv1	Download File View File

Crystal Structure of N-terminal domain of ArgZ, C264S mutant, bound to Substrate, an arginine dihydrolase from the Ornithine-Ammonia Cycle in Cyanobacteria

Zhuang, N., Li, L., Wu, X., Zhang, Y.

(2020) J Biological Chem 295: 2113-2124

Released	2020-01-15
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Synechocystis sp. PCC 6803 substr. Kazusa
Macromolecule	Sll1336 protein (protein)
Unique Ligands	ARG

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6LRF \| pdb_00006lrf	Download File View File

Crystal structure of unliganded AgrE

Lee, H., Rhee, S.

(2020) J Biological Chem 295: 5751-5760

Released	2020-04-01
Method	X-RAY DIFFRACTION 2.0546605257 Å
Organisms	Nostoc sp. PCC 7120 = FACHB-418
Macromolecule	Alr4995 protein (protein)

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6LRG \| pdb_00006lrg	Download File View File

Crystal Structure of the Ternary Complex of AgrE with Ornithine and NAD+

Lee, H., Rhee, S.

(2020) J Biological Chem 295: 5751-5760

Released	2020-04-01
Method	X-RAY DIFFRACTION 2.4121811586 Å
Organisms	Nostoc sp. PCC 7120 = FACHB-418
Macromolecule	Alr4995 protein (protein)
Unique Ligands	NAD, ORN

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6LRH \| pdb_00006lrh	Download File View File

Crystal Structure of the Binary Complex of AgrE C264A mutant with L-arginine

Lee, H., Rhee, S.

(2020) J Biological Chem 295: 5751-5760

Released	2020-04-01
Method	X-RAY DIFFRACTION 2.70510472826 Å
Organisms	Nostoc sp. PCC 7120 = FACHB-418
Macromolecule	Alr4995 protein (protein)
Unique Ligands	ARG

1 to 17 of 17 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

1U7H | pdb_00001u7h

Structure and a Proposed Mechanism for Ornithine Cyclodeaminase from Pseudomonas putida

1X7D | pdb_00001x7d

Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed with NAD and ornithine to 1.6 Angstroms

5GZI | pdb_00005gzi

Cyclodeaminase_PA

5GZJ | pdb_00005gzj

Cyclodeaminase_PA

5GZL | pdb_00005gzl

Cyclodeaminase_PA

5GZM | pdb_00005gzm

Cyclodeaminase_PA

5YU0 | pdb_00005yu0

Structural basis for recognition of L-lysine, L-ornithine, and L-2,4-diamino butyric acid by lysine cyclodeaminase

5YU1 | pdb_00005yu1

Structural basis for recognition of L-lysine, L-ornithine, and L-2,4-diamino butyric acid by lysine cyclodeaminase

5YU3 | pdb_00005yu3

Structural basis for recognition of L-lysine, L-ornithine, and L-2,4-diamino butyric acid by lysine cyclodeaminase

5YU4 | pdb_00005yu4

Structural basis for recognition of L-lysine, L-ornithine, and L-2,4-diamino butyric acid by lysine cyclodeaminase

6JUY | pdb_00006juy

Crystal Structure of ArgZ, apo structure, an Arginine Dihydrolase from the Ornithine-Ammonia Cycle in Cyanobacteria

6JUZ | pdb_00006juz

Crystal Structure of N-terminal domain of ArgZ(N71S) covalently bond to a reaction intermediate

6JV0 | pdb_00006jv0

Crystal Structure of N-terminal domain of ArgZ, bound to Product, an arginine dihydrolase from the Ornithine-Ammonia Cycle in Cyanobacteria

6JV1 | pdb_00006jv1

Crystal Structure of N-terminal domain of ArgZ, C264S mutant, bound to Substrate, an arginine dihydrolase from the Ornithine-Ammonia Cycle in Cyanobacteria

6LRF | pdb_00006lrf

Crystal structure of unliganded AgrE

6LRG | pdb_00006lrg

Crystal Structure of the Ternary Complex of AgrE with Ornithine and NAD+

6LRH | pdb_00006lrh

Crystal Structure of the Binary Complex of AgrE C264A mutant with L-arginine

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

1U7H | pdb_00001u7h

1X7D | pdb_00001x7d

5GZI | pdb_00005gzi

5GZJ | pdb_00005gzj

5GZL | pdb_00005gzl

5GZM | pdb_00005gzm

5YU0 | pdb_00005yu0

5YU1 | pdb_00005yu1

5YU3 | pdb_00005yu3

5YU4 | pdb_00005yu4

6JUY | pdb_00006juy

6JUZ | pdb_00006juz

6JV0 | pdb_00006jv0

6JV1 | pdb_00006jv1

6LRF | pdb_00006lrf

6LRG | pdb_00006lrg

6LRH | pdb_00006lrh