ANL Superfamily Solved Structures

In 2009, we published a review describing 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. At the time of the review, the list of ANL enzymes contained 16 unique proteins and 47 PDB entries. 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 March 2024. Currently 294 structures of 115 different proteins.

Protein

Organism

Conformation

PDBs and ligands or mutant structure
Luciferase P. pyralis Alternate 1LCI, unliganded; 1BA3, bromoform; 5DV9, unliganded;
C-terminal Domain Disordered 3IEP, unliganded; 3IER, PEG; 3IES, inhibitor; 3RIX, novel inhibitor.
Adenylate-forming 4G36, DLSA; 6Q2M, DLSA, mutant; 5KYT, DLSA, red mutant; 5KYV, DLSA, green mutant; 6HPS, iLuc Analog.
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; 5JRH, CoA + cAMP.
Acs S. cerevisiae Adenylation 1RY2, AMP.
CBAL 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, open 5C5H , OSB-AMP; 6NJ0 , OSB-mPhenyl-AMP.
o-Succinyl benzoylCoA ligase (MenE) B. subtilis Alternate/Adenylate/TE 5BUQ , unliganded; 5BUR , ATP; 5X8F , TE Conf AMP+SuccCoA; 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. 5ZRN , 1-OH-dodecyl-AMS.
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. 4IZ6 , Mech-Based inhibitor. Trap with ArCP, twinned.
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 Multiple States 4EAT, 4RLF, 4RLQ, 4RM2, 4RM3, 4RMN, 4ZJZ. 6M2T. 6M2O. 6M2U.
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 Partial 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).
Open 5U95 , unliganded.
AuaEII Stigmatella aurantiaca Adenylate-forming 4WV3 , Anthraniloyl-AMP.
FadD32 Mycobacterium smegmatis Adenylate-forming or cleaved 5D6N, N-term apo; 5D6J, full-length, ATP; 5EY8, AMPC20; 5ICR, Acyl-AMP.
ABBFA_003403 Acinetobacter baumannii Adenylate-forming 4ZXH , complete module; 4ZXI, module+AMP+Gly.
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, 5JNF. 6ULZ.
2019 Structures 6MFX, FATC; 6MFW, FATC; 6MFY, FATCA; 6MFZ, FATCAT; 6MG0, FATCA.
FadD32 Mycobacterium marinum Adenylate-forming 5EY9, acyl-AMP.
FadD32 Mycobacterium tuberculosis Adenylate-forming 5HM3, PhU-AMS.
PtmA2 Streptomyces platensis ~Adenylate-forming 5E7Q, apo.
Open 5UPQ, adenylate.
MbtA Mycobacterium smegmatis Intermediate 5KEI, apo.
Oxalyl-CoA Synthetase A. thaliana Adenylate-forming 5IE0, Oxalate.
Thr1 Synthetase Streptomyces sp. Oh-5093 Adenylate-forming 5N9X, ATP+threonine (chain A), AMP+Thr (chain B); 5N9W, unliganded.
Acetyl-CoA Synthetase Cryptococcus neoformans multiple conformations 5K85, Propyl-AMP; 5U29, acetyl-AMS; 5K8F, acetyl-AMP; 5IFI, Propyl-AMP; 5VPV, acetylated.
Acyl-CoA Synthetase Brucella canis Open 5U2A, unliganded.
IdnL1 Streptomyces sp. ML694-90F3 thioester-forming 5JJQ, b-aminoacyl-adenylate.
adenylate-forming 6AKD, Ala-AMS.>
CmiS6 Streptomyces sp MJ635-86F5 C-terminal Domain Disordered 5JJP, unliganded
PrpE Dinoroseobacter shibae Thioester-forming 5GXD, AMP, acrylate, and CoA.
Carboxylic Acid Reductase NRPS Nocardia iowensis Adenylate-forming 5MSC, AMP; 5MSD, benzoic acid.
Carboxylic Acid Reductase (NRPS) Segniliparus rugosus Adenylate-forming 5MST, AMP; 5MSW, Aden-PCP+AMP.
Thioester-forming 5MSS, Aden-PCP+AMP.
PqsA Pseudomonas aeruginosa N-terminal Domain Only 5OE3, Ant-AMP; 5OE4, Ant-AMP; 5OE5, Ant-AMP; 5OE6, 6F-Ant-AMP.
DhbF (MLP-Aden-PCP-Cond) Geobacillus Open Conformation 5U89, Gly-AVS.
TioS (A4a-ME-A4b) + TioT Micromonospora sp. ML1 TE Conformation + MLP 5WMM, Val-AMP. Interrupted Aden with ME.
TycA, engineered B. paribrevis C-term truncated 5N81, o-propargyl-bPhe-AMP; 5N82, bPhe-AMP.
McbA M. thermotolerans Adenylate 6H1B, Indolecarboxylate + AMP. 6SQ8, Indolecarboxylate + AMP.
Blue Shifted Luciferase A. vivianii Open 6AAA, unliganded.
Acetoacetyl-CoA Synthetase S. lividans Adenylate 4WD1, unliganded.
Propionyl-CoA Synthetase Erythrobacter sp. Large Multidomain multifunctional 6EQO, NADP+ADPcP.
Proto-luciferase Zophobas morio N-terminal Domain only 4W8O, PEG.
Txo1 Cond-Aden Eleftheria terrae Di-domain (C-A) 6OYF, Txo1, no C-term; 6OZV, Txo1, AMP+no C-term; 6P4U, Txo1, no C-term; 6P1J, Txo2, with C-term.
ObiF1 Burkholderia diffusa Adenylate 6N8E, Complete Module (CATTeMLP).
FscH Thermobifida fusca C-term Disordered 6EA3, Ser-AMP, Bound to MLP.
2HCL Aquincola tertiaricarbonis Multiple 6HDW, 2HIB-AMP (Aden); 6HDX, R3HIB-AMP (Aden); 6HDY, S3-HB-AMP (Aden); 6HE0, 2HIB-AMP + CoA (TE); 6HE2, 2HIB-AMP + CoA (open).
EntE Escherichia coli Thioester-Forming 6IYK, 2NB-AMS; 6HDX, 3CyanoB-AMS.
Methylmercaptopropionate-CoA Ligase Ruegeria lacuscaerulensis Multiple 6IHK, ADP (TE- and open); 6IJB, 3MMPA + AMP (Aden and open);
CahJ Micromonospora sp ML1 Thioester-forming 5WM2, Sal+AMP; 5WM3, Sal-AMP; 5WM4, 6MeSal-AMP; 5WM5, 5MeSal-AMP; 5WM6, Benzoyl-AMP; 5WM7, AMP.
PltF (+ PltL) P. protegens Thioester-forming 6O6E, A-PCP with Pro-AVS; 7THQ, PltF plus PigG with Pro-AVS;
CAR Aden GR01_22995 M. chelonae Adenylate-forming 6OZ1, AMP + Succinate;
NpsA K. oxytoca Multiple 6VHT, N-term Dom; 6VHU, N-term Dom; 6VHV, + 3HA-AMS; 6VHW, N-term Dom + 3HB-AMS; 6VHX, N-term Dom + 3HA-AMS; 6VHY, NpsA-ThdA Fusion + AVS; 6VHZ, N-term Dom + Ant-AMS.
Oxalyl-CoA Synthetase L. sativus Thioester 6QJZ, AMP.
FmoA3 Streptomyces sp Sp080513GE-23 Multidomain NRPS 6LTA, unliganded; 6LTB, AMPPNP; 6LTC, MeSer + AMP; 6LTD, MeSer + AMP.
StsA Bacillus stratosphericus Aden-KR-PCP 6ULW, Aden-KR didomain; 6ULX, adenylate; 6ULY, adenylate.
Acetyl-CoA Synthetase C. albicans Thioester 7KDS, propyl-AMP.
Acetyl-CoA Synthetase A. fumigatus Thioester 7KDN, propyl-AMP.
Acetyl-CoA Synthetase C. immitis Thioester 7KQ6, propyl-AMP.
Acetyl-CoA Synthetase C. posadasii Thioester 7KCP, propyl-AMP.
CfaL P. brasiliense Open 7A9J, R395G+CFA; 7A9I, CFA.
HitB-HitD E. scabrispora Thioester-forming 6M01, A-PCP complex; 7DQ5, Adenylate-forming, AMS; 7DQ6, Adenylate-forming; AMS inh.
Luciferase Lampyridae Adenylate-forming 6K4C, Ancient Lucif, Lucif-AMS.
Acs L. pneumonophila Thioester-forming 7MMZ, Ethyl-AMP.
BmdBC Thermoactinomyces vulgaris C-term disordered Complex of BmdB (Cy-A-T) with Oxidase. 7LY4, CryoEM BmdBC complex; 7LY5, BmdB fragment + BmdC; 7LY7, BmdB+BmdC complex.
PchE Pseudomonas aeruginosa Multiple CryoEM Structures of PchE, with ArCP-Cy-A-E-T architecture. 7EMY, 7EN1, 7EN2.
DltA Staphylococcus aureus Adenylate-forming 7VHV, ATP
PchD Pseudomonas aeruginosa Adenylate-forming 7TYB, Sal-AMS 7TZ4, CyanoSal-AMS
FAAL Synechococcus Adenylate-forming 7R7E, AMP+PPi; 7R7F, steroyl-adenylate.
DltA Lactiplantibacillus plantarum Adenylate-forming 7R27, AMP.
HitB+HitD Emblaya scabrispora Thioester-forming 6M01, crosslinker probe
Pls-A Streptomyces albulus Adenylate-forming 7WEW, bound to Lys-AMP
FadD23 Mycobacterium tuberculosis Adenylate-forming 8HD4, bound to palmitoyl-AMP; 8HDF, bound to AMPPNP; 8HCZ, N-term domain only.
PigI Serratia sp. ATCC39006 Thioester-forming 7THN, A-PCP didomain complex, with AVS.
CmnG Saccharothrix mutabilis Thioester-forming 7XBS, unliganded; 7XBT, ATP; 7XBU, capreomycidine; 7XBV, AMPPNP.
TycA Brevibacillus parabrevis Core domain only 7YWK, AMP; 7YWJ, L313P mutant.
FadD8 Mycobacteria tuberculosis Core domain only 8IVI, unliganded.
Tcp9 Actinoplanes teichomyceticus ACore domain 8GJ4, unliganded; 8GIC, HPG; 8GJP, core-ANC2; 8GKM, core-ANC3; 8GLC, core-ANC4.
McyB Microcystis aeruginosa Cond-Aden-core 8HLK, AMP+Leu.
PosA Acinetobacter baumannii Core domain only 8G95, unliganded; 8G96, L-Ornithine; 8G97, D-Ornithine; 8G98, Lysine.
AcylACP Synth Vibrio harveyi Aden-forming (hexameric ring) 8HSY, unliganded.
VinM-VinL Streptomyces halstedii Thioester-forming PCP complex 8K4R, holo-PCP.
GrsB1 Aneurinibacillus migulanus Acore 8P5O, unliganded.
HB-CoA Ligase Metallosphaera sedula TE-forming 8BIQ, AMP and acetyl-AMP.
AcsA Leishmania infantum TE-forming 8SF3, CoA + AMP + Acetate; 8U2T, CoA + AMP.

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

Please contact me ( ) with updates or corrections.
Studies in the Gulick Lab on NRPSs and Related proteins are supported by NIH Grant R35-GM136235.