4Q31

The crystal structure of cystathione gamma lyase (CalE6) from Micromonospora echinospora

PDB DOI: https://doi.org/10.2210/pdb4Q31/pdb

Classification: LYASE
Organism(s): Micromonospora echinospora
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-04-10 Released: 2014-05-07
Deposition Author(s): Tan, K., Bigelow, L., Jedrzejczak, R., Babnigg, G., Bingman, C.A., Yennamalli, R.M., Singh, S., Kharel, M.K., Thorson, J.S., Phillips Jr., G.N., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.191
R-Value Work: 0.152
R-Value Observed: 0.153

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural dynamics of a methionine gamma-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate.

Cao, H., Tan, K., Wang, F., Bigelow, L., Yennamalli, R.M., Jedrzejczak, R., Babnigg, G., Bingman, C.A., Joachimiak, A., Kharel, M.K., Singh, S., Thorson, J.S., Phillips, G.N.

(2016) Struct Dyn 3: 034702-034702

PubMed: 27191010 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1063/1.4948539
Primary Citation of Related Structures:
4Q31

PubMed Abstract:
CalE6 from Micromonospora echinospora is a (pyridoxal 5' phosphate) PLP-dependent methionine γ-lyase involved in the biosynthesis of calicheamicins. We report the crystal structure of a CalE6 2-(N-morpholino)ethanesulfonic acid complex showing ligand-induced rotation of Tyr100, which stacks with PLP, resembling the corresponding tyrosine rotation of true catalytic intermediates of CalE6 homologs. Elastic network modeling and crystallographic ensemble refinement reveal mobility of the N-terminal loop, which involves both tetrameric assembly and PLP binding. Modeling and comparative structural analysis of PLP-dependent enzymes involved in Cys/Met metabolism shine light on the functional implications of the intrinsic dynamic properties of CalE6 in catalysis and holoenzyme maturation.

Organizational Affiliation

Biosciences at Rice, Rice University , 6100 Main St., Houston, Texas 77005, USA.

Macromolecule Content

Total Structure Weight: 335.29 kDa
Atom Count: 24,719
Modelled Residue Count: 3,018
Deposited Residue Count: 3,072
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cystathione gamma lyase CalE6	A, B, C, D, E A, B, C, D, E, F, G, H	384	Micromonospora echinospora	Mutation(s): 1 Gene Names: calE6
UniProt
Find proteins for Q8KNG3 (Micromonospora echinospora) Explore Q8KNG3 Go to UniProtKB: Q8KNG3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8KNG3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain EB [auth H] SDF format, chain I [auth A] SDF format, chain KA [auth E] SDF format, chain Q [auth B] SDF format, chain QA [auth F] SDF format, chain WA [auth G] SDF format, chain Y [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain EB [auth H] MOL2 format, chain I [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain WA [auth G] MOL2 format, chain Y [auth C]	DA [auth D] EB [auth H] I [auth A] KA [auth E] Q [auth B] DA [auth D], EB [auth H], I [auth A], KA [auth E], Q [auth B], QA [auth F], WA [auth G], Y [auth C]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain EB [auth H] Focus chain I [auth A] Focus chain KA [auth E] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain WA [auth G] Focus chain Y [auth C] Interactions & Density Focus chain DA [auth D] Focus chain EB [auth H] Focus chain I [auth A] Focus chain KA [auth E] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain WA [auth G] Focus chain Y [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AB [auth G] SDF format, chain BA [auth C] SDF format, chain BB [auth G] SDF format, chain CB [auth G] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain HB [auth H] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth E] SDF format, chain N [auth A] SDF format, chain NA [auth E] SDF format, chain O [auth A] SDF format, chain OA [auth E] SDF format, chain PA [auth E] SDF format, chain S [auth B] SDF format, chain SA [auth F] SDF format, chain T [auth B] SDF format, chain TA [auth F] SDF format, chain U [auth B] SDF format, chain UA [auth F] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain YA [auth G] SDF format, chain ZA [auth G] MOL2 format, chain AB [auth G] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth G] MOL2 format, chain CB [auth G] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain HB [auth H] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain PA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain YA [auth G] MOL2 format, chain ZA [auth G]	AB [auth G] BA [auth C] BB [auth G] CB [auth G] GA [auth D] AB [auth G], BA [auth C], BB [auth G], CB [auth G], GA [auth D], HA [auth D], HB [auth H], IA [auth D], JA [auth D], L [auth A], M [auth A], MA [auth E], N [auth A], NA [auth E], O [auth A], OA [auth E], PA [auth E], S [auth B], SA [auth F], T [auth B], TA [auth F], U [auth B], UA [auth F], V [auth B], W [auth B], X [auth B], YA [auth G], ZA [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AB [auth G] Focus chain BA [auth C] Focus chain BB [auth G] Focus chain CB [auth G] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain HB [auth H] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth E] Focus chain N [auth A] Focus chain NA [auth E] Focus chain O [auth A] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth F] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain YA [auth G] Focus chain ZA [auth G] Interactions & Density Focus chain AB [auth G] Focus chain BA [auth C] Focus chain BB [auth G] Focus chain CB [auth G] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain HB [auth H] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth E] Focus chain N [auth A] Focus chain NA [auth E] Focus chain O [auth A] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth F] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain YA [auth G] Focus chain ZA [auth G]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DB [auth G] SDF format, chain IB [auth H] SDF format, chain P [auth A] SDF format, chain VA [auth F] MOL2 format, chain CA [auth C] MOL2 format, chain DB [auth G] MOL2 format, chain IB [auth H] MOL2 format, chain P [auth A] MOL2 format, chain VA [auth F]	CA [auth C], DB [auth G], IB [auth H], P [auth A], VA [auth F]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DB [auth G] Focus chain IB [auth H] Focus chain P [auth A] Focus chain VA [auth F] Interactions & Density Focus chain CA [auth C] Focus chain DB [auth G] Focus chain IB [auth H] Focus chain P [auth A] Focus chain VA [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain FB [auth H] SDF format, chain GB [auth H] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain LA [auth E] SDF format, chain R [auth B] SDF format, chain RA [auth F] SDF format, chain XA [auth G] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain FB [auth H] MOL2 format, chain GB [auth H] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain XA [auth G] MOL2 format, chain Z [auth C]	AA [auth C] EA [auth D] FA [auth D] FB [auth H] GB [auth H] AA [auth C], EA [auth D], FA [auth D], FB [auth H], GB [auth H], J [auth A], K [auth A], LA [auth E], R [auth B], RA [auth F], XA [auth G], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain FB [auth H] Focus chain GB [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain LA [auth E] Focus chain R [auth B] Focus chain RA [auth F] Focus chain XA [auth G] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain FB [auth H] Focus chain GB [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain LA [auth E] Focus chain R [auth B] Focus chain RA [auth F] Focus chain XA [auth G] Focus chain Z [auth C]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.191
R-Value Work: 0.152
R-Value Observed: 0.153
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.855	α = 90
b = 146.981	β = 90
c = 349.905	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing