PDBsum entry 3icd

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Oxidoreductase (NAD(a)-choh(d)) PDB id
Protein chain
414 a.a. *
Waters ×108
* Residue conservation analysis
PDB id:
Name: Oxidoreductase (NAD(a)-choh(d))
Title: Structure of a bacterial enzyme regulated by phosphorylation isocitrate dehydrogenase
Structure: Isocitrate dehydrogenase. Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562
Biol. unit: Dimer (from PQS)
2.50Å     R-factor:   0.180    
Authors: J.H.Hurley,P.E.Thorsness,V.Ramalingam,N.H.Helmers,D.E.Koshla R.M.Stroud
Key ref: J.H.Hurley et al. (1989). Structure of a bacterial enzyme regulated by phosphorylation, isocitrate dehydrogenase. Proc Natl Acad Sci U S A, 86, 8635-8639. PubMed id: 2682654 DOI: 10.1073/pnas.86.22.8635
28-Dec-89     Release date:   15-Jan-91    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P08200  (IDH_ECOLI) -  Isocitrate dehydrogenase [NADP]
416 a.a.
414 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Isocitrate dehydrogenase (NADP(+)).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Citric acid cycle
      Reaction: Isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH
+ NADP(+)
= 2-oxoglutarate
+ CO(2)
      Cofactor: Mn(2+) or Mg(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     oxidoreductase activity     6 terms  


DOI no: 10.1073/pnas.86.22.8635 Proc Natl Acad Sci U S A 86:8635-8639 (1989)
PubMed id: 2682654  
Structure of a bacterial enzyme regulated by phosphorylation, isocitrate dehydrogenase.
J.H.Hurley, P.E.Thorsness, V.Ramalingam, N.H.Helmers, D.E.Koshland, R.M.Stroud.
The structure of isocitrate dehydrogenase [threo-DS-isocitrate: NADP+ oxidoreductase (decarboxylating), EC] from Escherichia coli has been solved and refined at 2.5 A resolution and is topologically different from that of any other dehydrogenase. This enzyme, a dimer of identical 416-residue subunits, is inactivated by phosphorylation at Ser-113, which lies at the edge of an interdomain pocket that also contains many residues conserved between isocitrate dehydrogenase and isopropylmalate dehydrogenase. Isocitrate dehydrogenase contains an unusual clasp-like domain in which both polypeptide chains in the dimer interlock. Based on the structure of isocitrate dehydrogenase and conservation with isopropylmalate dehydrogenase, we suggest that the active site lies in an interdomain pocket close to the phosphorylation site.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20975740 B.Yang, C.Zhong, Y.Peng, Z.Lai, and J.Ding (2010).
Molecular mechanisms of "off-on switch" of activities of human IDH1 by tumor-associated mutation R132H.
  Cell Res, 20, 1188-1200.
PDB codes: 3map 3mar 3mas
20505668 J.Zheng, and Z.Jia (2010).
Structure of the bifunctional isocitrate dehydrogenase kinase/phosphatase.
  Nature, 465, 961-965.
PDB codes: 3eps 3lc6 3lcb
20516620 R.Malik, and R.E.Viola (2010).
Structural characterization of tartrate dehydrogenase: a versatile enzyme catalyzing multiple reactions.
  Acta Crystallogr D Biol Crystallogr, 66, 673-684.
PDB codes: 3flk 3fmx
20513808 Z.J.Reitman, and H.Yan (2010).
Isocitrate dehydrogenase 1 and 2 mutations in cancer: alterations at a crossroads of cellular metabolism.
  J Natl Cancer Inst, 102, 932-941.  
19274099 M.Aivaliotis, B.Macek, F.Gnad, P.Reichelt, M.Mann, and D.Oesterhelt (2009).
Ser/Thr/Tyr protein phosphorylation in the archaeon Halobacterium salinarum--a representative of the third domain of life.
  PLoS ONE, 4, e4777.  
  19052369 G.N.Hatzopoulos, G.Kefala, and J.Mueller-Dieckmann (2008).
Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analysis of isocitrate dehydrogenase 2 (Rv0066c) from Mycobacterium tuberculosis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 1139-1142.  
17634983 K.Imada, T.Tamura, R.Takenaka, I.Kobayashi, K.Namba, and K.Inagaki (2008).
Structure and quantum chemical analysis of NAD+-dependent isocitrate dehydrogenase: hydride transfer and co-factor specificity.
  Proteins, 70, 63-71.
PDB code: 2d4v
18203822 M.Aoshima, and Y.Igarashi (2008).
Nondecarboxylating and decarboxylating isocitrate dehydrogenases: oxalosuccinate reductase as an ancestral form of isocitrate dehydrogenase.
  J Bacteriol, 190, 2050-2055.  
18552125 Y.Peng, C.Zhong, W.Huang, and J.Ding (2008).
Structural studies of Saccharomyces cerevesiae mitochondrial NADP-dependent isocitrate dehydrogenase in different enzymatic states reveal substantial conformational changes during the catalytic reaction.
  Protein Sci, 17, 1542-1554.
PDB codes: 2qfv 2qfw 2qfx 2qfy
17160675 R.Stokke, D.Madern, A.E.Fedøy, S.Karlsen, N.K.Birkeland, and I.H.Steen (2007).
Biochemical characterization of isocitrate dehydrogenase from Methylococcus capsulatus reveals a unique NAD+-dependent homotetrameric enzyme.
  Arch Microbiol, 187, 361-370.  
17401542 R.Stokke, M.Karlström, N.Yang, I.Leiros, R.Ladenstein, N.K.Birkeland, and I.H.Steen (2007).
Thermal stability of isocitrate dehydrogenase from Archaeoglobus fulgidus studied by crystal structure analysis and engineering of chimers.
  Extremophiles, 11, 481-493.
PDB code: 2iv0
17123127 R.Stokke, N.K.Birkeland, and I.H.Steen (2007).
Thermal stability and biochemical properties of isocitrate dehydrogenase from the thermoacidophilic archaeon Thermoplasma acidophilum.
  Extremophiles, 11, 397-402.  
16416443 F.Imabayashi, S.Aich, L.Prasad, and L.T.Delbaere (2006).
Substrate-free structure of a monomeric NADP isocitrate dehydrogenase: an open conformation phylogenetic relationship of isocitrate dehydrogenase.
  Proteins, 63, 100-112.
PDB code: 2b0t
16362493 I.L.Jung, S.K.Kim, and I.G.Kim (2006).
The RpoS-mediated regulation of isocitrate dehydrogenase gene expression in Escherichia coli.
  Curr Microbiol, 52, 21-26.  
16897033 K.Murakami, R.Tsubouchi, M.Fukayama, T.Ogawa, and M.Yoshino (2006).
Oxidative inactivation of reduced NADP-generating enzymes in E. coli: iron-dependent inactivation with affinity cleavage of NADP-isocitrate dehydrogenase.
  Arch Microbiol, 186, 385-392.  
16759231 M.Karlström, I.H.Steen, D.Madern, A.E.Fedöy, N.K.Birkeland, and R.Ladenstein (2006).
The crystal structure of a hyperthermostable subfamily II isocitrate dehydrogenase from Thermotoga maritima.
  FEBS J, 273, 2851-2868.
PDB code: 1zor
16767773 O.V.Kalinina, and M.S.Gelfand (2006).
Amino acid residues that determine functional specificity of NADP- and NAD-dependent isocitrate and isopropylmalate dehydrogenases.
  Proteins, 64, 1001-1009.  
16284723 A.Rodríguez-Arnedo, M.Camacho, F.Llorca, and M.J.Bonete (2005).
Complete reversal of coenzyme specificity of isocitrate dehydrogenase from Haloferax volcanii.
  Protein J, 24, 259-266.  
  16511075 G.Hu, A.B.Taylor, L.McAlister-Henn, and P.J.Hart (2005).
Crystallization and preliminary X-ray crystallographic analysis of yeast NAD+-specific isocitrate dehydrogenase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 486-488.  
16166541 J.Miyazaki, K.Asada, S.Fushinobu, T.Kuzuyama, and M.Nishiyama (2005).
Crystal structure of tetrameric homoisocitrate dehydrogenase from an extreme thermophile, Thermus thermophilus: involvement of hydrophobic dimer-dimer interaction in extremely high thermotolerance.
  J Bacteriol, 187, 6779-6788.
PDB code: 1x0l
15146507 J.J.Jeong, T.Sonoda, S.Fushinobu, H.Shoun, and T.Wakagi (2004).
Crystal structure of isocitrate dehydrogenase from Aeropyrum pernix.
  Proteins, 55, 1087-1089.
PDB code: 1v94
12596267 T.Hamelryck (2003).
Efficient identification of side-chain patterns using a multidimensional index tree.
  Proteins, 51, 96.  
14568142 Z.X.Wang, C.Brämer, and A.Steinbüchel (2003).
Two phenotypically compensating isocitrate dehydrogenases in Ralstonia eutropha.
  FEMS Microbiol Lett, 227, 9.  
11992126 C.H.Williams, T.J.Stillman, V.V.Barynin, S.E.Sedelnikova, Y.Tang, J.Green, J.R.Guest, and P.J.Artymiuk (2002).
E. coli aconitase B structure reveals a HEAT-like domain with implications for protein-protein recognition.
  Nat Struct Biol, 9, 447-452.
PDB code: 1l5j
12204383 H.Inoue, T.Tamura, N.Ehara, A.Nishito, Y.Nakayama, M.Maekawa, K.Imada, H.Tanaka, and K.Inagaki (2002).
Biochemical and molecular characterization of the NAD(+)-dependent isocitrate dehydrogenase from the chemolithotroph Acidithiobacillus thiooxidans.
  FEMS Microbiol Lett, 214, 127-132.  
12454487 M.Karlström, I.H.Steen, G.Tibbelin, T.Lien, N.K.Birkeland, and R.Ladenstein (2002).
Crystallization and preliminary X-ray structure analysis of isocitrate dehydrogenase from two hyperthermophiles, Aeropyrum pernix and Thermotoga maritima.
  Acta Crystallogr D Biol Crystallogr, 58, 2162-2164.  
12005040 T.Sahara, Y.Takada, Y.Takeuchi, N.Yamaoka, and N.Fukunaga (2002).
Cloning, sequencing, and expression of a gene encoding the monomeric isocitrate dehydrogenase of the nitrogen-fixing bacterium, Azotobacter vinelandii.
  Biosci Biotechnol Biochem, 66, 489-500.  
11705966 G.D.Pullinger, R.Sowdhamini, and A.J.Lax (2001).
Localization of functional domains of the mitogenic toxin of Pasteurella multocida.
  Infect Immun, 69, 7839-7850.  
11455601 K.A.Denessiouk, V.V.Rantanen, and M.S.Johnson (2001).
Adenine recognition: a motif present in ATP-, CoA-, NAD-, NADP-, and FAD-dependent proteins.
  Proteins, 44, 282-291.  
11826966 M.Fujita, H.Tamegai, T.Eguchi, and K.Kakinuma (2001).
Novel substrate specificity of designer 3-isopropylmalate dehydrogenase derived from Thermus thermophilus HB8.
  Biosci Biotechnol Biochem, 65, 2695-2700.  
11679744 Y.Yasutake, S.Watanabe, M.Yao, Y.Takada, N.Fukunaga, and I.Tanaka (2001).
Crystallization and preliminary X-ray diffraction studies of monomeric isocitrate dehydrogenase by the MAD method using Mn atoms.
  Acta Crystallogr D Biol Crystallogr, 57, 1682-1685.  
10677231 C.Weiss, Y.Zeng, J.Huang, M.B.Sobocka, and J.I.Rushbrook (2000).
Bovine NAD+-dependent isocitrate dehydrogenase: alternative splicing and tissue-dependent expression of subunit 1.
  Biochemistry, 39, 1807-1816.  
10694384 N.B.Grodsky, S.Soundar, and R.F.Colman (2000).
Evaluation by site-directed mutagenesis of aspartic acid residues in the metal site of pig heart NADP-dependent isocitrate dehydrogenase.
  Biochemistry, 39, 2193-2200.  
  11206056 R.Chen, and S.S.Jeong (2000).
Functional prediction: identification of protein orthologs and paralogs.
  Protein Sci, 9, 2344-2353.  
10231385 C.Oudot, M.Jaquinod, J.C.Cortay, A.J.Cozzone, and J.M.Jault (1999).
The isocitrate dehydrogenase kinase/phosphatase from Escherichia coli is highly sensitive to in-vitro oxidative conditions role of cysteine67 and cysteine108 in the formation of a disulfide-bonded homodimer.
  Eur J Biochem, 262, 224-229.  
10489453 G.F.Audette, J.W.Quail, K.Hayakawa, C.Bai, R.Chen, and L.T.Delbaere (1999).
Crystallization and preliminary X-ray diffraction studies of monomeric isocitrate dehydrogenase from Corynebacterium glutamicum.
  Acta Crystallogr D Biol Crystallogr, 55, 1584-1585.  
10215879 J.Olano, J.Soler, F.Busto, and D.De Arriaga (1999).
Chemical modification of NADP-isocitrate dehydrogenase from Cephalosporium acremonium evidence of essential histidine and lysine groups at the active site.
  Eur J Biochem, 261, 640-649.  
10091606 S.M.Pitson, G.L.Mendz, S.Srinivasan, and S.L.Hazell (1999).
The tricarboxylic acid cycle of Helicobacter pylori.
  Eur J Biochem, 260, 258-267.  
9891796 A.J.Cozzone (1998).
Regulation of acetate metabolism by protein phosphorylation in enteric bacteria.
  Annu Rev Microbiol, 52, 127-164.  
9783749 B.L.Stoddard, B.E.Cohen, M.Brubaker, A.D.Mesecar, and D.E.Koshland (1998).
Millisecond Laue structures of an enzyme-product complex using photocaged substrate analogs.
  Nat Struct Biol, 5, 891-897.
PDB code: 1bl5
9818266 B.L.Stoddard (1998).
New results using Laue diffraction and time-resolved crystallography.
  Curr Opin Struct Biol, 8, 612-618.  
9532798 H.Matsunami, H.Kawaguchi, K.Inagaki, T.Eguchi, K.Kakinuma, and H.Tanaka (1998).
Overproduction and substrate specificity of 3-isopropylmalate dehydrogenase from Thiobacillus ferrooxidans.
  Biosci Biotechnol Biochem, 62, 372-373.  
9739088 K.Imada, K.Inagaki, H.Matsunami, H.Kawaguchi, H.Tanaka, N.Tanaka, and K.Namba (1998).
Structure of 3-isopropylmalate dehydrogenase in complex with 3-isopropylmalate at 2.0 A resolution: the role of Glu88 in the unique substrate-recognition mechanism.
  Structure, 6, 971-982.
PDB code: 1a05
9881153 M.Lancien, P.Gadal, and M.Hodges (1998).
Molecular characterization of higher plant NAD-dependent isocitrate dehydrogenase: evidence for a heteromeric structure by the complementation of yeast mutants.
  Plant J, 16, 325-333.  
9548941 M.Schutkowski, A.Bernhardt, X.Z.Zhou, M.Shen, U.Reimer, J.U.Rahfeld, K.P.Lu, and G.Fischer (1998).
Role of phosphorylation in determining the backbone dynamics of the serine/threonine-proline motif and Pin1 substrate recognition.
  Biochemistry, 37, 5566-5575.  
9211842 A.D.Mesecar, B.L.Stoddard, and D.E.Koshland (1997).
Orbital steering in the catalytic power of enzymes: small structural changes with large catalytic consequences.
  Science, 277, 202-206.
PDB codes: 1ai2 1ai3
9096353 A.M.Dean, and G.B.Golding (1997).
Protein engineering reveals ancient adaptive replacements in isocitrate dehydrogenase.
  Proc Natl Acad Sci U S A, 94, 3104-3109.  
9188741 A.V.Efimov (1997).
Structural trees for protein superfamilies.
  Proteins, 28, 241-260.  
9220992 B.E.Cohen, B.L.Stoddard, and D.E.Koshland (1997).
Caged NADP and NAD. Synthesis and characterization of functionally distinct caged compounds.
  Biochemistry, 36, 9035-9044.  
  9352899 F.S.Wang, T.S.Whittam, and R.K.Selander (1997).
Evolutionary genetics of the isocitrate dehydrogenase gene (icd) in Escherichia coli and Salmonella enterica.
  J Bacteriol, 179, 6551-6559.  
9354646 G.T.Jennings, K.I.Minard, and L.McAlister-Henn (1997).
Expression and mutagenesis of mammalian cytosolic NADP+-specific isocitrate dehydrogenase.
  Biochemistry, 36, 13743-13747.  
9428712 R.Chen, A.F.Greer, and A.M.Dean (1997).
Structural constraints in protein engineering--the coenzyme specificity of Escherichia coli isocitrate dehydrogenase.
  Eur J Biochem, 250, 578-582.  
  9023199 T.Suzuki, Y.Inoki, A.Yamagishi, T.Iwasaki, T.Wakagi, and T.Oshima (1997).
Molecular and phylogenetic characterization of isopropylmalate dehydrogenase of a thermoacidophilic archaeon, Sulfolobus sp. strain 7.
  J Bacteriol, 179, 1174-1179.  
  8745412 A.M.Dean, A.K.Shiau, and D.E.Koshland (1996).
Determinants of performance in the isocitrate dehydrogenase of Escherichia coli.
  Protein Sci, 5, 341-347.  
8885829 B.Sankaran, A.J.Chavan, and B.E.Haley (1996).
Identification of adenine binding domain peptides of the NADP+ active site within porcine heart NADP(+)-dependent isocitrate dehydrogenase.
  Biochemistry, 35, 13501-13510.  
8639526 J.H.Hurley, R.Chen, and A.M.Dean (1996).
Determinants of cofactor specificity in isocitrate dehydrogenase: structure of an engineered NADP+ --> NAD+ specificity-reversal mutant.
  Biochemistry, 35, 5670-5678.
PDB code: 1iso
  8953733 K.Miyazaki (1996).
Isocitrate dehydrogenase from Thermus aquaticus YT1: purification of the enzyme and cloning, sequencing, and expression of the gene.
  Appl Environ Microbiol, 62, 4627-4631.  
  8763933 M.I.Muro-Pastor, J.C.Reyes, and F.J.Florencio (1996).
The NADP+-isocitrate dehydrogenase gene (icd) is nitrogen regulated in cyanobacteria.
  J Bacteriol, 178, 4070-4076.  
8608121 M.J.Brubaker, D.H.Dyer, B.Stoddard, and D.E.Koshland (1996).
Synthesis, kinetics, and structural studies of a photolabile caged isocitrate: a catalytic trigger for isocitrate dehydrogenase.
  Biochemistry, 35, 2854-2864.  
8901552 R.Chen, A.Greer, and A.M.Dean (1996).
Redesigning secondary structure to invert coenzyme specificity in isopropylmalate dehydrogenase.
  Proc Natl Acad Sci U S A, 93, 12171-12176.  
  8745407 R.Chen, J.A.Grobler, J.H.Hurley, and A.M.Dean (1996).
Second-site suppression of regulatory phosphorylation in Escherichia coli isocitrate dehydrogenase.
  Protein Sci, 5, 287-295.
PDB codes: 1gro 1grp
8552589 S.Jones, and J.M.Thornton (1996).
Principles of protein-protein interactions.
  Proc Natl Acad Sci U S A, 93, 13-20.  
  8535253 A.M.Dean, and L.Dvorak (1995).
The role of glutamate 87 in the kinetic mechanism of Thermus thermophilus isopropylmalate dehydrogenase.
  Protein Sci, 4, 2156-2167.  
  16535052 J.Olano, Arriaga, F.Busto, and J.Soler (1995).
Kinetics and Thermostability of NADP-Isocitrate Dehydrogenase from Cephalosporium acremonium.
  Appl Environ Microbiol, 61, 2326-2334.  
  7536733 M.Suzuki, T.Sahara, J.Tsuruha, Y.Takada, and N.Fukunaga (1995).
Differential expression in Escherichia coli of the Vibrio sp. strain ABE-1 icdI and icdII genes encoding structurally different isocitrate dehydrogenase isozymes.
  J Bacteriol, 177, 2138-2142.  
  7795532 R.Sowdhamini, and T.L.Blundell (1995).
An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins.
  Protein Sci, 4, 506-520.  
8076632 A.Chavanieu, N.E.Keane, P.G.Quirk, B.A.Levine, B.Calas, L.Wei, and L.Ellis (1994).
Phosphorylation effects on flanking charged residues. Structural implications for signal transduction in protein kinases.
  Eur J Biochem, 224, 115-123.  
7881901 J.H.Hurley, and A.M.Dean (1994).
Structure of 3-isopropylmalate dehydrogenase in complex with NAD+: ligand-induced loop closing and mechanism for cofactor specificity.
  Structure, 2, 1007-1016.
PDB code: 1hex
8181473 K.Miyazaki, T.Yaoi, and T.Oshima (1994).
Expression, purification, and substrate specificity of isocitrate dehydrogenase from Thermus thermophilus HB8.
  Eur J Biochem, 221, 899-903.  
  8169222 M.I.Muro-Pastor, and F.J.Florencio (1994).
NADP(+)-isocitrate dehydrogenase from the cyanobacterium Anabaena sp. strain PCC 7120: purification and characterization of the enzyme and cloning, sequencing, and disruption of the icd gene.
  J Bacteriol, 176, 2718-2726.  
7874731 Q.Xie, and A.Jiménez (1994).
Cloning and molecular analysis of two different ILV5 genes from a brewing strain of Saccharomyces cerevisiae.
  Curr Genet, 26, 398-402.  
  8226630 A.Ishii, M.Suzuki, T.Sahara, Y.Takada, S.Sasaki, and N.Fukunaga (1993).
Genes encoding two isocitrate dehydrogenase isozymes of a psychrophilic bacterium, Vibrio sp. strain ABE-1.
  J Bacteriol, 175, 6873-6880.  
8433976 B.L.Stoddard, and D.E.Koshland (1993).
Molecular recognition analyzed by docking simulations: the aspartate receptor and isocitrate dehydrogenase from Escherichia coli.
  Proc Natl Acad Sci U S A, 90, 1146-1153.  
8381789 D.C.LaPorte (1993).
The isocitrate dehydrogenase phosphorylation cycle: regulation and enzymology.
  J Cell Biochem, 51, 14-18.  
8467073 M.K.Udvardi, T.R.McDermott, and M.L.Kahn (1993).
Isolation and characterization of a cDNA encoding NADP(+)-specific isocitrate dehydrogenase from soybean (Glycine max).
  Plant Mol Biol, 21, 739-752.  
  7508076 M.Riley (1993).
Functions of the gene products of Escherichia coli.
  Microbiol Rev, 57, 862-952.  
  1539996 K.Miyazaki, H.Eguchi, A.Yamagishi, T.Wakagi, and T.Oshima (1992).
Molecular cloning of the isocitrate dehydrogenase gene of an extreme thermophile, Thermus thermophilus HB8.
  Appl Environ Microbiol, 58, 93-98.  
1730247 M.I.Muro-Pastor, and F.J.Florencio (1992).
Purification and properties of NADP-isocitrate dehydrogenase from the unicellular cyanobacterium Synechocystis sp. PCC 6803.
  Eur J Biochem, 203, 99.  
1935983 M.L.Leyland, and D.J.Kelly (1991).
Purification and characterization of a monomeric isocitrate dehydrogenase with dual coenzyme specificity from the photosynthetic bacterium Rhodomicrobium vannielii.
  Eur J Biochem, 202, 85-93.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.