ANL Super Family Solved Structures

In 2009, we published a review concerning the Conformational dynamics of members of the ANL Superfamily of enzymes. The review contained a table that listed PDB coordinates for structurally characterized members of this family of adenylating enzymes. This page will attempt to keep this list up-to-date, with links to the coordinates and references at the Protein Data Bank. (See note at bottom of table regarding references).

Updated September, 2016. Currently 148 structures of 58 different proteins.

Protein

Organism

Conformation

PDBs and ligands or mutant structure

Luciferase

P. pyralis

Alternate

1LCI, unliganded; 1BA3, bromoform.

C-terminal Domain Disordered

3IEP, unliganded; 3IER, PEG; 3IES, inhibitor; 3RIX, novel inhibitor.

Adenylate-forming

4G36, DLSA.

Oxidative (TE-forming)

4G37, chemically cross-linked + DLSA.

PheA

B. brevis

Adenylation

1AMU, AMP + Phe.

DhbE

B. subtilis

Adenylation

1MDF, unliganded; 1MD9, AMP + DHB; 1MDB, DHB-AMP adenylate.

Acs

S. enterica

Thioester

1PG4, adenosine-5-propylphosphate + CoA; 1PG3, same ligands, acetylated on Lys609; 2P2F, acetate, AMP, COA; 2P20, R584A; 2P2B, V386A; 2P2J, K609A; 2P2M, R194A; 2P2Q, R584E.

Acs

S. cerevisiae

Adenylation

1RY2, AMP.

CBL

A. sp AL3007

Adenylation

1T5H, unliganded; 1T5D, 4CB; 2QVX, 2QVY, I303G; 2QVZ, 2QW0, I303A; 3CW8, 4CB-AMP; 3DLP, D402P.

Thioester

3CW9, 4CPh-CoA + AMP.

Fatty Acs

T. thermophilus

Aden/Alternate

1ULT, unliganded.

Thioester

1V25, AMPPNP; 1V26, Myristyl-AMP.

Luciferase

L. cruciata

Adenylation

2D1Q, AMP; 2D1R, oxyluciferin + AMP; 2D1S, N-(dehydroluciferyl)sulfamoyl adenosine; 2D1T, T217I.

Benzoyl-CL

B. xenovorans

Adenylation

2V7B , benzoic acid.

Med. Acs

H. sapiens

Adenylation

3C5E , ATP; 3DAY , AMPCPP; 3GPC , CoA.

Thioester

2WD9 , ibuprofin; 2VZE , AMP; 3EQ6 , butyryl-CoA + AMP; 3B7W , unliganded.

SrfA-C

B. subtilis

~Adenylation

2VSQ , Leucine bound to multidomain NRPS.

DltA

B. cereus

Adenylation

3DHV , alanyl-AMP; 3FCC , Mg ATP; 3FCE, Ca ATP. 4PZP, unliganded.

DltA

B. subtilis

Thioester

3E7W , AMP; 3E7X , AMP.

AAE

M. acetivorans

Thioester

3ETC , unliganded.

FAAL28

M. tuberculosis

N-terminal domain only

3E53 , unliganded; 3T5A , G330W mutant.

Fatty Acs

A. fulgidus

Alternate

3G7S , unliganded.

PaaK1

B. cenocepacia

Adenylation

2Y27 , ATP; 2Y4N , PhenylacetylAMP.

PaaK2

B. cenocepacia

Thioester

2Y4O , phenylacetyl adenylate.

4Coumarate CoA Ligase

P. tomentosa

Alternate

3A9U , unliganded.

Thioester

3A9V, AMP. 3NI2, Adenylate inhibitor.

o-Succinyl benzoylCoA ligase

S. aureus

Alternate

3IPL , unliganded.

o-Succinyl benzoylCoA ligase (MenE)

E. coli

Adenylate

5C5H , OSB-AMP.

o-Succinyl benzoylCoA ligase (MenE)

B. subtilis

Alternate/Adenylate

5BUQ , unliganded;

5BUR , ATP; 5BUS , AMP.

SidN

N. lolii

Disordered and Alternate

3ITE , unliganded.

FAAL

R. palustrus

Cterm disordered

3IVR , unliganded.

FAAL

E. coli

Adenylate

3PBK , acyl-adenylate.

FAAL

L. pneumophilia

Alternate

3KXW , FA adenylate; 3LNV , FA adenylate + PPi.

Ala-polyphosphoribitol ligase

S. pyogenes

Adenylation

3L8C , unliganded; 3LGX , ATP.

EhpF

P. agglomerans

No C-terminal domain

3L2K , phenazine dicarboxylate.

Malonyl-CoA Ligase

S. coelicolor

thioester

3NYQ , AMP + MeMalonyl-CoA; 3NYR , AMP + Malonyl-CoA.

BasE

A. baumannii

C-term disordered

3O82 , Adenylate Inh; 3O83 , Adenylate Inh; 3O84 , HTS Inh8; 3U16, HTS Inh67; 3U17, HTS Inh70.

4-Coumaroyl-CoA Ligase: Stilbene Synthase Fusion

A. thaliana

C-term disordered

3TSY , Fusion Protein.

FAAL13

M. tuberculosis

C-term disordered or cleaved

3T5B , unliganded; 3T5C , unliganded.

Alternate

3R44 , None in Active Site.

Luciferase

L. turkestanicus

C-term disordered

3QYA , Red-emitter; 4M46 , Green-emitter;

EntE-B Fusion

E. coli

thioester

3RG2 , Mech-Based inhibitor. Trap with ArCP.

PA1221

P. aearuginosa

thioester

4DG8 , AMP + cryo; 4DG9 , Mech-Based inhibitor. Trap with PCP.

MatB

R. palustris

Adenylate

4FUQ , unliganded; 4FUT , ATP; 4GXQ , ATP/chimeric; 4GXR , ATP.

Phenylacetate:CoA Ligase

B. thetaiotaomicron

Multiple

4RVN , AMP+CoA; 4RVO , CoA; 4R1M , AMP; 4R1L , ADP/AMP.

CytC1

Streptomyces sp.

Adenylate

3VNR , ADP; 3VNS , Val+AMP; 3VNQ , ATP.

FadD10

M. tuberculosis

Alternate

4IR7, FA-AMP; 4ISB, unlig.

BaiB, Bile acid CoA ligase

C. scindens

C-term Disordered

4LGC, Unliganded.

Benzoate CoA Ligase

R. palustris

Thioester-forming

Multipe States: 4EAT, 4RLF, 4RLQ, 4RM2, 4RM3, 4RMN, 4ZJZ.

Odd, small family member

D. fermentans

Very Open, dimeric

4GS5,unliganded.

Acs C-term only

S. enterica

Complex with PAT

4U5Y,protein-protein complex.

VinN

Streptomyces halstedtii

Cterm truncated/disordered

3WVN,L-Aspartate; 3WV5,3-MeAsp; 3WV4,unliganded.

ApnA A1

P. agardhii

Partiall disordered or TE-forming

4D4G, AMPPNP; 4D4H, Apo; 4D4I, AMPPNP + Arg; 4D56, Tyr-AMP; 4D57, Arg-AMP.

AlmE

V. cholera

Thioester-forming

4OXI , Gly-AMP.

McyG

Mycrocystis aeruginosa

Adenylate-forming

4R0M , Aden-PCP.

4-Coumarate:CoA Ligase

Nicotiana tabacum

Adenylate-forming

5BSM , ATP.

Thioester-forming

5BSR , AMP+CoA; 5BST , Coumaroyl-AMP; 5BSU , Caffeoyl-AMP; 5BSV , Feruoyl-AMP; 5BSW , feruoyl-AMP (V341Mut).

AuaEII

Stigmatella aurantiaca

Adenylate-forming

4WV3 , Anthraniloyl-AMP.

FadD32

Mycobacterium smegmatis

Adenylate-forming or cleaved

5D6N , N-term apo; 5D6J, full-length, ATP.

ABBFA_003403

Acinetobacter baumannii

Adenylate-forming

4ZXH , complete module; 4ZXI, module+adenylate.

EntF

E. coli

Thioester-forming

5T3D , complete module, Ser-AVS. ;5JA1, complete module + YbdZ ;5JA2, complete module + PA2412.

LgrA

Brevibacillus parabrevis

Initiation module (FT-A-PCP)

Multiple States: 5ES5, 5ES6, 5ES7, 5ES8, 5ES9.

FadD32

Mycobacterium smegmatis

Adenylate-forming

5EY8, AMPC20.

FadD32

Mycobacterium marinum

Adenylate-forming

5EY9, acyl-AMP.

FadD32

Mycobacterium tuberculosis

Adenylate-forming

5HM3, PhU-AMS.

PtmA2

Streptomyces platensis

~Adenylate-forming

5E7Q, apo.

MbtA

Mycobacterium smegmatis

~Intermediate

5KEI, apo.

Some of the structures were determined in our lab, while others have been determined by other crystallographers throughout the world. References to publications are available at the links at the Protein Data Bank.

Please contact me ( ) with updates or corrections.