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(-) Description

Title :  ACC DEAMINASE MUTANT COMPLEXED WITH ACC
 
Authors :  T. Ose, A. Fujino, M. Yao, M. Honma, I. Tanaka
Date :  12 Nov 02  (Deposition) - 12 May 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Plp Dependent B Group, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Ose, A. Fujino, M. Yao, N. Watanabe, M. Honma, I. Tanaka
Reaction Intermediate Structures Of 1-Aminocyclopropane-1-Carboxylate Deaminase: Insight Into Plp-Dependent Cyclopropane Ring-Opening Reaction
J. Biol. Chem. V. 278 41069 2003
PubMed-ID: 12882962  |  Reference-DOI: 10.1074/JBC.M305865200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE
    ChainsA, B, C, D
    EC Number4.1.99.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET11D
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    MutationYES
    Organism ScientificWILLIOPSIS SATURNUS
    Organism Taxid4906
    SynonymACCD, ACC DEAMINASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
15PA4Ligand/IonN-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-Y-LMETHYL]-1-AMINO-CYCLOPROPANECARBOXYLIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
15PA2Ligand/IonN-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-Y-LMETHYL]-1-AMINO-CYCLOPROPANECARBOXYLIC ACID
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
15PA2Ligand/IonN-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-Y-LMETHYL]-1-AMINO-CYCLOPROPANECARBOXYLIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:54 , GLY A:74 , GLY A:75 , SER A:78 , ASN A:79 , GLN A:80 , TRP A:102 , ALA A:163 , GLY A:164 , SER A:166 , CYS A:200 , VAL A:201 , THR A:202 , GLY A:203 , SER A:204 , THR A:205 , TYR A:295 , GLU A:296 , HOH A:1467 , HOH A:1477BINDING SITE FOR RESIDUE 5PA A 1401
2AC2SOFTWAREASN B:50 , LYS B:54 , SER B:78 , ASN B:79 , GLN B:80 , GLY B:164 , CYS B:200 , VAL B:201 , THR B:202 , GLY B:203 , SER B:204 , THR B:205 , TYR B:295 , GLU B:296 , LEU B:323 , GLY B:324 , GLY B:325 , HOH B:1507 , HOH B:1574BINDING SITE FOR RESIDUE 5PA B 1501
3AC3SOFTWAREASN C:50 , LYS C:54 , SER C:78 , ASN C:79 , GLN C:80 , GLY C:164 , CYS C:200 , VAL C:201 , THR C:202 , GLY C:203 , THR C:205 , TYR C:295 , GLU C:296 , LEU C:323 , GLY C:324 , GLY C:325 , HOH C:1603 , HOH C:1611 , HOH C:1734 , HOH C:1736BINDING SITE FOR RESIDUE 5PA C 1601
4AC4SOFTWAREASN D:50 , LYS D:54 , SER D:78 , ASN D:79 , GLN D:80 , ALA D:163 , GLY D:164 , VAL D:201 , THR D:202 , GLY D:203 , SER D:204 , THR D:205 , TYR D:295 , GLU D:296 , LEU D:323 , GLY D:324 , GLY D:325 , HOH D:1710 , HOH D:1760 , HOH D:1820BINDING SITE FOR RESIDUE 5PA D 1701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J0D)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:266 -Pro A:267
2Tyr B:266 -Pro B:267
3Tyr C:266 -Pro C:267
4Tyr D:266 -Pro D:267

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J0D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J0D)

(-) Exons   (0, 0)

(no "Exon" information available for 1J0D)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:341
 aligned with 1A1D_CYBSA | Q7M523 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:341
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340 
           1A1D_CYBSA     1 SGVAKFAKYPLTFGPSPISNLNRLSQHLGSKVNVYAKREDCNSGLAFGGNKLRKLEYIVPDIVEGDYTHLVSIGGRQSNQTRMVAALAAKLGKKCVLIQEDWVPIPEAEKDVYNRVGNIELSRIMGADVRVIEDGFDIGMRKSFANALQELEDAGHKPYPIPAGCSEHKYGGLGFVGFADEVINQEVELGIKFDKIVVCCVTGSTTAGILAGMAQYGRQDDVIAIDASFTSEKTKEQTLRIANNTAKLIGVEHEFKDFTLDTRFAYPCYGVPNEGTIEAIRTCAEQEGVLTDPVYEGKSMQGLIALIKEDYFKPGANVLYVHLGGAPALSAYSSFFPTKTA 341
               SCOP domains d1j0da_ A: 1-aminocyclopropane-1-carboxylate deaminase                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1j0dA01 A:1-45,A:168-341                     --------------------1j0dA02 A:66-167  [code=3.40.50.1100, no name defined]                                                1j0dA01 A:1-45,A:168-341  [code=3.40.50.1100, no name defined]                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeehhhhhhhh...eeeeeee.hhh......hhhhhhhh.hhhhhhhh...eeeeeee...hhhhhhhhhhhhhh.eeeeeee.....hhhhh.....hhhhhhhhhh..eeee.........hhhhhhhhhhhhhh....eeehhhhh.....hhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhhhhhhh.........ee...........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh......eeeeeee..hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j0d A   1 AGVAKFAKYPLTFGPSPISNLNRLSQHLGSKVNVYAKREDCNSGLAFGGNTLRKLEYIVPDIVEGDYTHLVSIGGRQSNQTRMVAALAAKLGKKCVLIQEDWVPIPEAEKDVYNRVGNIELSRIMGADVRVIEDGFDIGMRKSFANALQELEDAGHKPYPIPAGCSEHKYGGLGFVGFADEVINQEVELGIKFDKIVVCCVTGSTTAGILAGMAQYGRQDDVIAIDASFTSEKTKEQTLRIANNTAKLIGVEHEFKDFTLDTRFAYPCYGVPNEGTIEAIRTCAEQEGVLTDPVYEGKSMQGLIALIKEDYFKPGANVLYVHLGGAPALSAYSSFFPTKTA 341
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340 

Chain B from PDB  Type:PROTEIN  Length:341
 aligned with 1A1D_CYBSA | Q7M523 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:341
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340 
           1A1D_CYBSA     1 SGVAKFAKYPLTFGPSPISNLNRLSQHLGSKVNVYAKREDCNSGLAFGGNKLRKLEYIVPDIVEGDYTHLVSIGGRQSNQTRMVAALAAKLGKKCVLIQEDWVPIPEAEKDVYNRVGNIELSRIMGADVRVIEDGFDIGMRKSFANALQELEDAGHKPYPIPAGCSEHKYGGLGFVGFADEVINQEVELGIKFDKIVVCCVTGSTTAGILAGMAQYGRQDDVIAIDASFTSEKTKEQTLRIANNTAKLIGVEHEFKDFTLDTRFAYPCYGVPNEGTIEAIRTCAEQEGVLTDPVYEGKSMQGLIALIKEDYFKPGANVLYVHLGGAPALSAYSSFFPTKTA 341
               SCOP domains d1j0db_ B: 1-aminocyclopropane-1-carboxylate deaminase                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1j0dB01 B:1-45,B:168-341                     --------------------1j0dB02 B:66-167  [code=3.40.50.1100, no name defined]                                                1j0dB01 B:1-45,B:168-341  [code=3.40.50.1100, no name defined]                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................ee.hhhhhhhh....eeeeee.hhh......hhhhhhhh.hhhhhhhh...eeee.ee..hhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhhhhhhhhhh..eee............hhhhhhhhhhhh...eeeehhhhh.....hhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j0d B   1 AGVAKFAKYPLTFGPSPISNLNRLSQHLGSKVNVYAKREDCNSGLAFGGNTLRKLEYIVPDIVEGDYTHLVSIGGRQSNQTRMVAALAAKLGKKCVLIQEDWVPIPEAEKDVYNRVGNIELSRIMGADVRVIEDGFDIGMRKSFANALQELEDAGHKPYPIPAGCSEHKYGGLGFVGFADEVINQEVELGIKFDKIVVCCVTGSTTAGILAGMAQYGRQDDVIAIDASFTSEKTKEQTLRIANNTAKLIGVEHEFKDFTLDTRFAYPCYGVPNEGTIEAIRTCAEQEGVLTDPVYEGKSMQGLIALIKEDYFKPGANVLYVHLGGAPALSAYSSFFPTKTA 341
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340 

Chain C from PDB  Type:PROTEIN  Length:341
 aligned with 1A1D_CYBSA | Q7M523 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:341
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340 
           1A1D_CYBSA     1 SGVAKFAKYPLTFGPSPISNLNRLSQHLGSKVNVYAKREDCNSGLAFGGNKLRKLEYIVPDIVEGDYTHLVSIGGRQSNQTRMVAALAAKLGKKCVLIQEDWVPIPEAEKDVYNRVGNIELSRIMGADVRVIEDGFDIGMRKSFANALQELEDAGHKPYPIPAGCSEHKYGGLGFVGFADEVINQEVELGIKFDKIVVCCVTGSTTAGILAGMAQYGRQDDVIAIDASFTSEKTKEQTLRIANNTAKLIGVEHEFKDFTLDTRFAYPCYGVPNEGTIEAIRTCAEQEGVLTDPVYEGKSMQGLIALIKEDYFKPGANVLYVHLGGAPALSAYSSFFPTKTA 341
               SCOP domains d1j0dc_ C: 1-aminocyclopropane-1-carboxylate deaminase                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1j0dC01 C:1-45,C:168-341                     --------------------1j0dC02 C:66-167  [code=3.40.50.1100, no name defined]                                                1j0dC01 C:1-45,C:168-341  [code=3.40.50.1100, no name defined]                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeehhhhhhhh...eeeeeee.hhh......hhhhhhhh..hhhhhh....eeeeeee..hhhhhhhhhhhhhh..eeeeeee.....hhhhh.....hhhhhhhhhh..eeee.........hhhhhhhhhhhhhh...eeeehhhhh......hhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhhhhhhh........eee...........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh......eeeeeee..hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j0d C   1 AGVAKFAKYPLTFGPSPISNLNRLSQHLGSKVNVYAKREDCNSGLAFGGNTLRKLEYIVPDIVEGDYTHLVSIGGRQSNQTRMVAALAAKLGKKCVLIQEDWVPIPEAEKDVYNRVGNIELSRIMGADVRVIEDGFDIGMRKSFANALQELEDAGHKPYPIPAGCSEHKYGGLGFVGFADEVINQEVELGIKFDKIVVCCVTGSTTAGILAGMAQYGRQDDVIAIDASFTSEKTKEQTLRIANNTAKLIGVEHEFKDFTLDTRFAYPCYGVPNEGTIEAIRTCAEQEGVLTDPVYEGKSMQGLIALIKEDYFKPGANVLYVHLGGAPALSAYSSFFPTKTA 341
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340 

Chain D from PDB  Type:PROTEIN  Length:341
 aligned with 1A1D_CYBSA | Q7M523 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:341
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340 
           1A1D_CYBSA     1 SGVAKFAKYPLTFGPSPISNLNRLSQHLGSKVNVYAKREDCNSGLAFGGNKLRKLEYIVPDIVEGDYTHLVSIGGRQSNQTRMVAALAAKLGKKCVLIQEDWVPIPEAEKDVYNRVGNIELSRIMGADVRVIEDGFDIGMRKSFANALQELEDAGHKPYPIPAGCSEHKYGGLGFVGFADEVINQEVELGIKFDKIVVCCVTGSTTAGILAGMAQYGRQDDVIAIDASFTSEKTKEQTLRIANNTAKLIGVEHEFKDFTLDTRFAYPCYGVPNEGTIEAIRTCAEQEGVLTDPVYEGKSMQGLIALIKEDYFKPGANVLYVHLGGAPALSAYSSFFPTKTA 341
               SCOP domains d1j0dd_ D: 1-aminocyclopropane-1-carboxylate deaminase                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1j0dD01 D:1-45,D:168-341                     --------------------1j0dD02 D:66-167  [code=3.40.50.1100, no name defined]                                                1j0dD01 D:1-45,D:168-341  [code=3.40.50.1100, no name defined]                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...........eeehhhhhhhh...eeeeeee.hhh......hhhhhhhh.hhhhhhhh...eeeeeee..hhhhhhhhhhhhhhh.eeeeeee.....hhhhh.....hhhhhhhhhh..eeee.........hhhhhhhhhhhhhh...eeeehhhhh......hhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhhhhhhh........eee...........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh......eeeeeee..hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j0d D   1 AGVAKFAKYPLTFGPSPISNLNRLSQHLGSKVNVYAKREDCNSGLAFGGNTLRKLEYIVPDIVEGDYTHLVSIGGRQSNQTRMVAALAAKLGKKCVLIQEDWVPIPEAEKDVYNRVGNIELSRIMGADVRVIEDGFDIGMRKSFANALQELEDAGHKPYPIPAGCSEHKYGGLGFVGFADEVINQEVELGIKFDKIVVCCVTGSTTAGILAGMAQYGRQDDVIAIDASFTSEKTKEQTLRIANNTAKLIGVEHEFKDFTLDTRFAYPCYGVPNEGTIEAIRTCAEQEGVLTDPVYEGKSMQGLIALIKEDYFKPGANVLYVHLGGAPALSAYSSFFPTKTA 341
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340 

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric Unit

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
1a1j0dA01A:1-45,A:168-341
1b1j0dA02A:66-167
1c1j0dB02B:66-167
1d1j0dC02C:66-167
1e1j0dD02D:66-167
1f1j0dB01B:1-45,B:168-341
1g1j0dC01C:1-45,C:168-341
1h1j0dD01D:1-45,D:168-341

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J0D)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (1A1D_CYBSA | Q7M523)
molecular function
    GO:0008660    1-aminocyclopropane-1-carboxylate deaminase activity    Catalysis of the reaction: 1-aminocyclopropane-1-carboxylate + H(2)O = 2-oxobutanate + NH(4)(+).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
biological process
    GO:0009310    amine catabolic process    The chemical reactions and pathways resulting in the breakdown of any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        1A1D_CYBSA | Q7M5231f2d 1j0c 1j0e

(-) Related Entries Specified in the PDB File

1f2d ACC DEAMINASE FROM HANSENULA SATURNUS
1j0a CRYSTAL STRUCTURE ANALYSIS OF THE ACC DEAMINASE HOMOLOGUE
1j0b ACC DEAMINASE HOMOLOGURE COMPLEXED WITH INHIITOR
1j0c ACC DEAMINASE MUTATED TO CATALYTIC RESIDUE
1j0e ACC DEAMINASE MUTANT REACTON INTERMEDIATE