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9IAM

Structure of cyclodipeptide synthase from nocardia brasiliensis (nbra-cdps) in complex with alanylated rna microhelices analogues mimicking ala-trna-ala substrate

PDB DOI: 10.2210/pdb9iam/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Nocardia Brasiliensis Atcc 700358 , Synthetic Construct

Deposited: 2025-02-11
Deposition Author(s): Charbonnier, J.B. , Fernandez Varela, P. , Legrand, P. , Marouf, Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.61 Å

Literature

Structure of cyclodipeptide synthase from nocardia brasiliensis (nbra-cdps) in complex with alanylated rna microhelices analogues mimicking ala-trna-ala substrate

Charbonnier, J.B. , Fernandez Varela, P. , Legrand, P. , Marouf, Z.

Primary Citation of Related Structures: 9IAM


Proteins
Molecule Chains Sequence Length Organism Sequence
Cyclodipeptide synthase A 248 Nocardia Brasiliensis Atcc 700358 , Synthetic Construct MATTTTLLSASHKAAYDLRSDGITTDGRSTVLLVAVGADYHEGEKLAATIDLINRSNFGRVSIAVADTLQRHNLSGGTDIDRHARARIAGDEWIARNSTLLDRIDCPTNVLRWDFALSHPRYGDLYDAVEHAYETDEPYRHAIDSTIDRFIERRLSREPDVDQESVRKACRAYLLEECPIIMPLWAHEGFDFVIYPQRISAAMGRTRELFVVPEHPDRVAWLPLRFKKRKSALHGAREEQRSHHHHHH
Cyclodipeptide synthase B 248 Nocardia Brasiliensis Atcc 700358 , Synthetic Construct MATTTTLLSASHKAAYDLRSDGITTDGRSTVLLVAVGADYHEGEKLAATIDLINRSNFGRVSIAVADTLQRHNLSGGTDIDRHARARIAGDEWIARNSTLLDRIDCPTNVLRWDFALSHPRYGDLYDAVEHAYETDEPYRHAIDSTIDRFIERRLSREPDVDQESVRKACRAYLLEECPIIMPLWAHEGFDFVIYPQRISAAMGRTRELFVVPEHPDRVAWLPLRFKKRKSALHGAREEQRSHHHHHH
Cyclodipeptide synthase C 248 Nocardia Brasiliensis Atcc 700358 , Synthetic Construct MATTTTLLSASHKAAYDLRSDGITTDGRSTVLLVAVGADYHEGEKLAATIDLINRSNFGRVSIAVADTLQRHNLSGGTDIDRHARARIAGDEWIARNSTLLDRIDCPTNVLRWDFALSHPRYGDLYDAVEHAYETDEPYRHAIDSTIDRFIERRLSREPDVDQESVRKACRAYLLEECPIIMPLWAHEGFDFVIYPQRISAAMGRTRELFVVPEHPDRVAWLPLRFKKRKSALHGAREEQRSHHHHHH
Cyclodipeptide synthase D 248 Nocardia Brasiliensis Atcc 700358 , Synthetic Construct MATTTTLLSASHKAAYDLRSDGITTDGRSTVLLVAVGADYHEGEKLAATIDLINRSNFGRVSIAVADTLQRHNLSGGTDIDRHARARIAGDEWIARNSTLLDRIDCPTNVLRWDFALSHPRYGDLYDAVEHAYETDEPYRHAIDSTIDRFIERRLSREPDVDQESVRKACRAYLLEECPIIMPLWAHEGFDFVIYPQRISAAMGRTRELFVVPEHPDRVAWLPLRFKKRKSALHGAREEQRSHHHHHH
Cyclodipeptide synthase E 248 Nocardia Brasiliensis Atcc 700358 , Synthetic Construct MATTTTLLSASHKAAYDLRSDGITTDGRSTVLLVAVGADYHEGEKLAATIDLINRSNFGRVSIAVADTLQRHNLSGGTDIDRHARARIAGDEWIARNSTLLDRIDCPTNVLRWDFALSHPRYGDLYDAVEHAYETDEPYRHAIDSTIDRFIERRLSREPDVDQESVRKACRAYLLEECPIIMPLWAHEGFDFVIYPQRISAAMGRTRELFVVPEHPDRVAWLPLRFKKRKSALHGAREEQRSHHHHHH
Cyclodipeptide synthase F 248 Nocardia Brasiliensis Atcc 700358 , Synthetic Construct MATTTTLLSASHKAAYDLRSDGITTDGRSTVLLVAVGADYHEGEKLAATIDLINRSNFGRVSIAVADTLQRHNLSGGTDIDRHARARIAGDEWIARNSTLLDRIDCPTNVLRWDFALSHPRYGDLYDAVEHAYETDEPYRHAIDSTIDRFIERRLSREPDVDQESVRKACRAYLLEECPIIMPLWAHEGFDFVIYPQRISAAMGRTRELFVVPEHPDRVAWLPLRFKKRKSALHGAREEQRSHHHHHH
Cyclodipeptide synthase G 248 Nocardia Brasiliensis Atcc 700358 , Synthetic Construct MATTTTLLSASHKAAYDLRSDGITTDGRSTVLLVAVGADYHEGEKLAATIDLINRSNFGRVSIAVADTLQRHNLSGGTDIDRHARARIAGDEWIARNSTLLDRIDCPTNVLRWDFALSHPRYGDLYDAVEHAYETDEPYRHAIDSTIDRFIERRLSREPDVDQESVRKACRAYLLEECPIIMPLWAHEGFDFVIYPQRISAAMGRTRELFVVPEHPDRVAWLPLRFKKRKSALHGAREEQRSHHHHHH
Cyclodipeptide synthase H 248 Nocardia Brasiliensis Atcc 700358 , Synthetic Construct MATTTTLLSASHKAAYDLRSDGITTDGRSTVLLVAVGADYHEGEKLAATIDLINRSNFGRVSIAVADTLQRHNLSGGTDIDRHARARIAGDEWIARNSTLLDRIDCPTNVLRWDFALSHPRYGDLYDAVEHAYETDEPYRHAIDSTIDRFIERRLSREPDVDQESVRKACRAYLLEECPIIMPLWAHEGFDFVIYPQRISAAMGRTRELFVVPEHPDRVAWLPLRFKKRKSALHGAREEQRSHHHHHH
Cyclodipeptide synthase I 248 Nocardia Brasiliensis Atcc 700358 , Synthetic Construct MATTTTLLSASHKAAYDLRSDGITTDGRSTVLLVAVGADYHEGEKLAATIDLINRSNFGRVSIAVADTLQRHNLSGGTDIDRHARARIAGDEWIARNSTLLDRIDCPTNVLRWDFALSHPRYGDLYDAVEHAYETDEPYRHAIDSTIDRFIERRLSREPDVDQESVRKACRAYLLEECPIIMPLWAHEGFDFVIYPQRISAAMGRTRELFVVPEHPDRVAWLPLRFKKRKSALHGAREEQRSHHHHHH
Cyclodipeptide synthase J 248 Nocardia Brasiliensis Atcc 700358 , Synthetic Construct MATTTTLLSASHKAAYDLRSDGITTDGRSTVLLVAVGADYHEGEKLAATIDLINRSNFGRVSIAVADTLQRHNLSGGTDIDRHARARIAGDEWIARNSTLLDRIDCPTNVLRWDFALSHPRYGDLYDAVEHAYETDEPYRHAIDSTIDRFIERRLSREPDVDQESVRKACRAYLLEECPIIMPLWAHEGFDFVIYPQRISAAMGRTRELFVVPEHPDRVAWLPLRFKKRKSALHGAREEQRSHHHHHH
Cyclodipeptide synthase K 248 Nocardia Brasiliensis Atcc 700358 , Synthetic Construct MATTTTLLSASHKAAYDLRSDGITTDGRSTVLLVAVGADYHEGEKLAATIDLINRSNFGRVSIAVADTLQRHNLSGGTDIDRHARARIAGDEWIARNSTLLDRIDCPTNVLRWDFALSHPRYGDLYDAVEHAYETDEPYRHAIDSTIDRFIERRLSREPDVDQESVRKACRAYLLEECPIIMPLWAHEGFDFVIYPQRISAAMGRTRELFVVPEHPDRVAWLPLRFKKRKSALHGAREEQRSHHHHHH
Cyclodipeptide synthase L 248 Nocardia Brasiliensis Atcc 700358 , Synthetic Construct MATTTTLLSASHKAAYDLRSDGITTDGRSTVLLVAVGADYHEGEKLAATIDLINRSNFGRVSIAVADTLQRHNLSGGTDIDRHARARIAGDEWIARNSTLLDRIDCPTNVLRWDFALSHPRYGDLYDAVEHAYETDEPYRHAIDSTIDRFIERRLSREPDVDQESVRKACRAYLLEECPIIMPLWAHEGFDFVIYPQRISAAMGRTRELFVVPEHPDRVAWLPLRFKKRKSALHGAREEQRSHHHHHH
Cyclodipeptide synthase M 248 Nocardia Brasiliensis Atcc 700358 , Synthetic Construct MATTTTLLSASHKAAYDLRSDGITTDGRSTVLLVAVGADYHEGEKLAATIDLINRSNFGRVSIAVADTLQRHNLSGGTDIDRHARARIAGDEWIARNSTLLDRIDCPTNVLRWDFALSHPRYGDLYDAVEHAYETDEPYRHAIDSTIDRFIERRLSREPDVDQESVRKACRAYLLEECPIIMPLWAHEGFDFVIYPQRISAAMGRTRELFVVPEHPDRVAWLPLRFKKRKSALHGAREEQRSHHHHHH
Cyclodipeptide synthase N 248 Nocardia Brasiliensis Atcc 700358 , Synthetic Construct MATTTTLLSASHKAAYDLRSDGITTDGRSTVLLVAVGADYHEGEKLAATIDLINRSNFGRVSIAVADTLQRHNLSGGTDIDRHARARIAGDEWIARNSTLLDRIDCPTNVLRWDFALSHPRYGDLYDAVEHAYETDEPYRHAIDSTIDRFIERRLSREPDVDQESVRKACRAYLLEECPIIMPLWAHEGFDFVIYPQRISAAMGRTRELFVVPEHPDRVAWLPLRFKKRKSALHGAREEQRSHHHHHH

Nucleic Acids / Hybrid
Molecule Chains Sequence Length Organism Sequence
RNA (5'-R(P*GP*GP*GP*GP*CP*UP*AP*UP*UP*CP*GP*UP*AP*GP*CP*UP*CP*CP*AP*CP*C)-3') o 22 NA GGGGCUAUUCGUAGCUCCACCX
RNA (5'-R(P*GP*GP*GP*GP*CP*UP*AP*UP*UP*CP*GP*UP*AP*GP*CP*UP*CP*CP*AP*CP*C)-3') p 22 NA GGGGCUAUUCGUAGCUCCACCX
RNA (5'-R(P*GP*GP*GP*GP*CP*UP*AP*UP*UP*CP*GP*UP*AP*GP*CP*UP*CP*CP*AP*CP*C)-3') r 22 NA GGGGCUAUUCGUAGCUCCACCX
RNA (5'-R(P*GP*GP*GP*GP*CP*UP*AP*UP*UP*CP*GP*UP*AP*GP*CP*UP*CP*CP*AP*CP*C)-3') q 22 NA GGGGCUAUUCGUAGCUCCACCX
RNA (5'-R(P*GP*GP*GP*GP*CP*UP*AP*UP*UP*CP*GP*UP*AP*GP*CP*UP*CP*CP*AP*CP*C)-3') t 22 NA GGGGCUAUUCGUAGCUCCACCX
Experimental Data

Method: X-RAY DIFFRACTION

Deposited Date: 2025-02-11
Deposition Author(s): Charbonnier, J.B. , Fernandez Varela, P. , Legrand, P. , Marouf, Z.