2Z8Y | pdb_00002z8y

Xenon-bound structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase(CODH/ACS) from Moorella thermoacetica

PDB DOI: https://doi.org/10.2210/pdb2Z8Y/pdb

Classification: Oxidoreductase/Transferase
Organism(s): Neomoorella thermoacetica
Mutation(s): No

Deposited: 2007-09-12 Released: 2008-03-11
Deposition Author(s): Doukov, T.I., Blasiak, L.C., Drennan, C.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free:
0.250 (Depositor)
R-Value Work:
0.178 (Depositor), 0.179 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Xenon in and at the End of the Tunnel of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase

Doukov, T.I., Blasiak, L.C., Seravalli, J., Ragsdale, S.W., Drennan, C.L.

(2008) Biochemistry 47: 3474-3483

PubMed: 18293927 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/bi702386t
Primary Citation Related Structures:
2Z8Y

PubMed Abstract:
A fascinating feature of some bifunctional enzymes is the presence of an internal channel or tunnel to connect the multiple active sites. A channel can allow for a reaction intermediate generated at one active site to be used as a substrate at a second active site, without the need for the intermediate to leave the safety of the protein matrix. One such bifunctional enzyme is carbon monoxide dehydrogenase/acetyl-CoA synthase from Moorella thermoacetica (mtCODH/ACS). A key player in the global carbon cycle, CODH/ACS uses a Ni-Fe-S center called the C-cluster to reduce carbon dioxide to carbon monoxide and uses a second Ni-Fe-S center, called the A-cluster, to assemble acetyl-CoA from a methyl group, coenzyme A, and C-cluster-generated CO. mtCODH/ACS has been proposed to contain one of the longest enzyme channels (138 A long) to allow for intermolecular CO transport. Here, we report a 2.5 A resolution structure of xenon-pressurized mtCODH/ACS and examine the nature of gaseous cavities within this enzyme. We find that the cavity calculation program CAVENV accurately predicts the channels connecting the C- and A-clusters, with 17 of 19 xenon binding sites within the predicted regions. Using this X-ray data, we analyze the amino acid composition surrounding the 19 Xe sites and consider how the protein fold is utilized to carve out such an impressive interior passageway. Finally, structural comparisons of Xe-pressurized mtCODH/ACS with related enzyme structures allow us to study channel design principles, as well as consider the conformational flexibility of an enzyme that contains a cavity through its center.

Organizational Affiliation

Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

Macromolecule Content

Total Structure Weight: 630.94 kDa
Atom Count: 44,706
Modeled Residue Count: 5,603
Deposited Residue Count: 5,612
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon monoxide dehydrogenase/acetyl CoA synthase subunit beta	A, B, C, D	674	Neomoorella thermoacetica	Mutation(s): 0 EC: 1.2.7.4 (PDB Primary Data), 1.2.99.2 (PDB Primary Data)
UniProt
Find proteins for P27989 (Neomoorella thermoacetica) Explore P27989 Go to UniProtKB: P27989
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27989
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon monoxide dehydrogenase/acetyl CoA synthase subunit alpha	E [auth M], F [auth N], G [auth O], H [auth P]	729	Neomoorella thermoacetica	Mutation(s): 0 EC: 2.3.1.169
UniProt
Find proteins for P27988 (Neomoorella thermoacetica) Explore P27988 Go to UniProtKB: P27988
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27988
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XCC Query on XCC Download:Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain SA [auth D] SDF format, chain W [auth B] SDF format, chain K [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain SA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain K [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain SA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain K [auth A]	IA [auth C], K [auth A], SA [auth D], W [auth B]	FE(4)-NI(1)-S(4) CLUSTER Fe₄ Ni S₄ QGLWBXDZIHZONR-UHFFFAOYSA-N		Interactions Focus chain IA [auth C] Focus chain K [auth A] Focus chain SA [auth D] Focus chain W [auth B] Interactions & Density Focus chain IA [auth C] Focus chain K [auth A] Focus chain SA [auth D] Focus chain W [auth B]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JB [auth N] SDF format, chain WB [auth P] SDF format, chain V [auth B] SDF format, chain RA [auth D] SDF format, chain QB [auth O] SDF format, chain HA [auth C] SDF format, chain DB [auth M] MOL2 format, chain GA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JB [auth N] MOL2 format, chain WB [auth P] MOL2 format, chain V [auth B] MOL2 format, chain RA [auth D] MOL2 format, chain QB [auth O] MOL2 format, chain HA [auth C] MOL2 format, chain DB [auth M] mmCIF format, chain GA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JB [auth N] mmCIF format, chain WB [auth P] mmCIF format, chain V [auth B] mmCIF format, chain RA [auth D] mmCIF format, chain QB [auth O] mmCIF format, chain HA [auth C] mmCIF format, chain DB [auth M]	DB [auth M] GA [auth C] HA [auth C] I [auth A] J [auth A] DB [auth M], GA [auth C], HA [auth C], I [auth A], J [auth A], JB [auth N], QB [auth O], RA [auth D], V [auth B], WB [auth P]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain DB [auth M] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain JB [auth N] Focus chain QB [auth O] Focus chain RA [auth D] Focus chain V [auth B] Focus chain WB [auth P] Interactions & Density Focus chain DB [auth M] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain JB [auth N] Focus chain QB [auth O] Focus chain RA [auth D] Focus chain V [auth B] Focus chain WB [auth P]
XE Query on XE Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AC [auth P] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain EB [auth M] SDF format, chain FB [auth M] SDF format, chain GB [auth M] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain KB [auth N] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain LB [auth N] SDF format, chain MB [auth N] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain NB [auth N] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain RB [auth O] SDF format, chain SB [auth O] SDF format, chain TA [auth D] SDF format, chain TB [auth O] SDF format, chain VA [auth D] SDF format, chain WA [auth D] SDF format, chain X [auth B] SDF format, chain XA [auth D] SDF format, chain XB [auth P] SDF format, chain Y [auth B] SDF format, chain YA [auth D] SDF format, chain Z [auth B] SDF format, chain ZB [auth P] SDF format, chain YB [auth P] SDF format, chain UA [auth D] SDF format, chain MA [auth C] SDF format, chain M [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain AC [auth P] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain EB [auth M] MOL2 format, chain FB [auth M] MOL2 format, chain GB [auth M] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain KB [auth N] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain LB [auth N] MOL2 format, chain MB [auth N] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain NB [auth N] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain RB [auth O] MOL2 format, chain SB [auth O] MOL2 format, chain TA [auth D] MOL2 format, chain TB [auth O] MOL2 format, chain VA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain XB [auth P] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain ZB [auth P] MOL2 format, chain YB [auth P] MOL2 format, chain UA [auth D] MOL2 format, chain MA [auth C] MOL2 format, chain M [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain AC [auth P] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain EB [auth M] mmCIF format, chain FB [auth M] mmCIF format, chain GB [auth M] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain KB [auth N] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain LB [auth N] mmCIF format, chain MB [auth N] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain NB [auth N] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain RB [auth O] mmCIF format, chain SB [auth O] mmCIF format, chain TA [auth D] mmCIF format, chain TB [auth O] mmCIF format, chain VA [auth D] mmCIF format, chain WA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth D] mmCIF format, chain XB [auth P] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain ZB [auth P] mmCIF format, chain YB [auth P] mmCIF format, chain UA [auth D] mmCIF format, chain MA [auth C] mmCIF format, chain M [auth A]	AA [auth B] AC [auth P] BA [auth B] CA [auth B] EB [auth M] AA [auth B], AC [auth P], BA [auth B], CA [auth B], EB [auth M], FB [auth M], GB [auth M], JA [auth C], KA [auth C], KB [auth N], L [auth A], LA [auth C], LB [auth N], M [auth A], MA [auth C], MB [auth N], N [auth A], NA [auth C], NB [auth N], O [auth A], OA [auth C], P [auth A], Q [auth A], RB [auth O], SB [auth O], TA [auth D], TB [auth O], UA [auth D], VA [auth D], WA [auth D], X [auth B], XA [auth D], XB [auth P], Y [auth B], YA [auth D], YB [auth P], Z [auth B], ZB [auth P]	XENON Xe FHNFHKCVQCLJFQ-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AC [auth P] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain EB [auth M] Focus chain FB [auth M] Focus chain GB [auth M] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain KB [auth N] Focus chain L [auth A] Focus chain LA [auth C] Focus chain LB [auth N] Focus chain M [auth A] Focus chain MA [auth C] Focus chain MB [auth N] Focus chain N [auth A] Focus chain NA [auth C] Focus chain NB [auth N] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain Q [auth A] Focus chain RB [auth O] Focus chain SB [auth O] Focus chain TA [auth D] Focus chain TB [auth O] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain XB [auth P] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain YB [auth P] Focus chain Z [auth B] Focus chain ZB [auth P] Interactions & Density Focus chain AA [auth B] Focus chain AC [auth P] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain EB [auth M] Focus chain FB [auth M] Focus chain GB [auth M] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain KB [auth N] Focus chain L [auth A] Focus chain LA [auth C] Focus chain LB [auth N] Focus chain M [auth A] Focus chain MA [auth C] Focus chain MB [auth N] Focus chain N [auth A] Focus chain NA [auth C] Focus chain NB [auth N] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain Q [auth A] Focus chain RB [auth O] Focus chain SB [auth O] Focus chain TA [auth D] Focus chain TB [auth O] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain XB [auth P] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain YB [auth P] Focus chain Z [auth B] Focus chain ZB [auth P]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain U [auth A] SDF format, chain ZA [auth D] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain AB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain ZA [auth D] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain AB [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain PA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain ZA [auth D] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain AB [auth D]	AB [auth D] DA [auth B] EA [auth B] FA [auth B] PA [auth C] AB [auth D], DA [auth B], EA [auth B], FA [auth B], PA [auth C], QA [auth C], R [auth A], S [auth A], T [auth A], U [auth A], ZA [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AB [auth D] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain ZA [auth D] Interactions & Density Focus chain AB [auth D] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain ZA [auth D]
CU1 Query on CU1 Download:Ideal Coordinates CCD File SDF format, chain HB [auth N] SDF format, chain OB [auth O] SDF format, chain UB [auth P] SDF format, chain BB [auth M] MOL2 format, chain HB [auth N] MOL2 format, chain OB [auth O] MOL2 format, chain UB [auth P] MOL2 format, chain BB [auth M] mmCIF format, chain HB [auth N] mmCIF format, chain OB [auth O] mmCIF format, chain UB [auth P] mmCIF format, chain BB [auth M]	BB [auth M], HB [auth N], OB [auth O], UB [auth P]	COPPER (I) ION Cu VMQMZMRVKUZKQL-UHFFFAOYSA-N		Interactions Focus chain BB [auth M] Focus chain HB [auth N] Focus chain OB [auth O] Focus chain UB [auth P] Interactions & Density Focus chain BB [auth M] Focus chain HB [auth N] Focus chain OB [auth O] Focus chain UB [auth P]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain CB [auth M] SDF format, chain IB [auth N] SDF format, chain PB [auth O] SDF format, chain VB [auth P] MOL2 format, chain CB [auth M] MOL2 format, chain IB [auth N] MOL2 format, chain PB [auth O] MOL2 format, chain VB [auth P] mmCIF format, chain CB [auth M] mmCIF format, chain IB [auth N] mmCIF format, chain PB [auth O] mmCIF format, chain VB [auth P]	CB [auth M], IB [auth N], PB [auth O], VB [auth P]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain CB [auth M] Focus chain IB [auth N] Focus chain PB [auth O] Focus chain VB [auth P] Interactions & Density Focus chain CB [auth M] Focus chain IB [auth N] Focus chain PB [auth O] Focus chain VB [auth P]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free: 0.250 (Depositor)
R-Value Work: 0.178 (Depositor), 0.179 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.54	α = 101.29
b = 136.6	β = 109.22
c = 141.75	γ = 103.91

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-03-11

Deposition Author(s):

Doukov, T.I.

Blasiak, L.C.

Drennan, C.L.

Revision History (Full details and data files)

Version 1.0: 2008-03-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2014-11-12
Changes: Structure summary
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description