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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE ACC DEAMINASE HOMOLOGUE
 
Authors :  A. Fujino, T. Ose, M. Honma, M. Yao, I. Tanaka
Date :  12 Nov 02  (Deposition) - 12 May 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  A (2x),B (2x),C (2x)
Keywords :  Plp Dependent, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Fujino, T. Ose, M. Yao, T. Tokiwano, M. Honma, N. Watanabe, I. Tanaka
Structural And Enzymatic Properties Of 1-Aminocyclopropane-1-Carboxylate Deaminase Homologue From Pyrococcus Horikoshii
J. Mol. Biol. V. 341 999 2004
PubMed-ID: 15328614  |  Reference-DOI: 10.1016/J.JMB.2004.06.062

(-) Compounds

Molecule 1 - 1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE
    Chains: A, B, C
    EC Number: 4.1.99.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3
    Synonym: AHP, ACC DEAMINASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): A  
Biological Unit 2 (1x):  BC
Biological Unit 3 (2x): A (2x)B (2x)C (2x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1IPA1Ligand/IonISOPROPYL ALCOHOL
2PLP3Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SO43Ligand/IonSULFATE ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1IPA2Ligand/IonISOPROPYL ALCOHOL
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1IPA-1Ligand/IonISOPROPYL ALCOHOL
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SO42Ligand/IonSULFATE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1IPA-1Ligand/IonISOPROPYL ALCOHOL
2PLP-1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SO4-1Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:54 , SER A:81 , ASN A:82 , HIS A:83 , TYR A:256 , TYR A:282 , PLP A:401 , HOH A:1752 , HOH A:1782BINDING SITE FOR RESIDUE SO4 A 701
2AC2SOFTWARELYS B:54 , SER B:81 , ASN B:82 , HIS B:83 , GLY B:157 , TYR B:256 , TYR B:282 , PLP B:501 , HOH B:725BINDING SITE FOR RESIDUE SO4 B 702
3AC3SOFTWARELYS C:54 , SER C:81 , ASN C:82 , HIS C:83 , GLY C:157 , TYR C:256 , TYR C:282 , PLP C:601 , HOH C:724BINDING SITE FOR RESIDUE SO4 C 703
4AC4SOFTWAREASN A:53 , LYS A:54 , LYS A:57 , ASN A:82 , ALA A:189 , GLY A:190 , SER A:191 , GLY A:192 , GLY A:193 , THR A:194 , TYR A:282 , THR A:308 , GLY A:309 , GLY A:310 , SO4 A:701 , HOH A:1748 , HOH A:1769BINDING SITE FOR RESIDUE PLP A 401
5AC5SOFTWAREASN B:53 , LYS B:54 , LYS B:57 , ASN B:82 , ALA B:189 , GLY B:190 , SER B:191 , GLY B:192 , GLY B:193 , THR B:194 , TYR B:282 , THR B:308 , GLY B:309 , GLY B:310 , SO4 B:702 , HOH B:705BINDING SITE FOR RESIDUE PLP B 501
6AC6SOFTWAREASN C:53 , LYS C:54 , LYS C:57 , ASN C:82 , ALA C:189 , GLY C:190 , SER C:191 , GLY C:192 , GLY C:193 , THR C:194 , TYR C:282 , THR C:308 , GLY C:309 , GLY C:310 , SO4 C:703 , HOH C:712 , HOH C:713BINDING SITE FOR RESIDUE PLP C 601
7AC7SOFTWAREPHE A:12 , ARG A:14 , ARG C:14BINDING SITE FOR RESIDUE IPA A 1747

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J0A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J0A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J0A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J0A)

(-) Exons   (0, 0)

(no "Exon" information available for 1J0A)

(-) 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:325
 aligned with 1A1D_PYRHO | O57809 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:325
                                    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     
           1A1D_PYRHO     1 MHPKIFALLAKFPRVELIPWETPIQYLPNISREIGADVYIKRDDLTGLGIGGNKIRKLEYLLGDALSKGADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLRGKEELKGNYLLDKIMGIETRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGASPIGTLGYVRAVGEIATQSEVKFDSIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIKEAAELLGVKVEVRPELYDYSFGEYGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGLVDLARKGELGEKILFIHTGGISGTFHYGDKLLSLL 325
               SCOP domains d1j0aa_ A: 1-aminocyclopropane-1-carboxylate deaminase                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1j0aA01 A:1-52,A:158-325                            1j0aA02 A:53-156  [code=3.40.50.1100, no name defined]                                                  -1j0aA01 A:1-52,A:158-325  [code=3.40.50.1100, no name defined]                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.............eeehhhhhhhhh.eeeeee.hhh......hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhh..eeeee......hhhhhhhhhhhhhh.....eeeehhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhh........eeee.........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j0a A   1 MHPKIFALLAKFPRVELIPWETPIQYLPNISREIGADVYIKRDDLTGLGIGGNKIRKLEYLLGDALSKGADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLRGKEELKGNYLLDKIMGIETRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGASPIGTLGYVRAVGEIATQSEVKFDSIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIKEAAELLGVKVEVRPELYDYSFGEYGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGLVDLARKGELGEKILFIHTGGISGTFHYGDKLLSLL 325
                                    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     


Chain B from PDB  Type:PROTEIN  Length:325
 aligned with 1A1D_PYRHO | O57809 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:325
                                    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     
           1A1D_PYRHO     1 MHPKIFALLAKFPRVELIPWETPIQYLPNISREIGADVYIKRDDLTGLGIGGNKIRKLEYLLGDALSKGADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLRGKEELKGNYLLDKIMGIETRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGASPIGTLGYVRAVGEIATQSEVKFDSIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIKEAAELLGVKVEVRPELYDYSFGEYGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGLVDLARKGELGEKILFIHTGGISGTFHYGDKLLSLL 325
               SCOP domains d1j0ab_ B: 1-aminocyclopropane-1-carboxylate deaminase                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1j0aB01 B:1-52,B:158-325                            1j0aB02 B:53-156  [code=3.40.50.1100, no name defined]                                                  -1j0aB01 B:1-52,B:158-325  [code=3.40.50.1100, no name defined]                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.............eeehhhhhhhhh.eeeeee.hhh......hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh..eeeee.......hhhhhhhhhh..ee..........hhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhhhh.......eeee.........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j0a B   1 MHPKIFALLAKFPRVELIPWETPIQYLPNISREIGADVYIKRDDLTGLGIGGNKIRKLEYLLGDALSKGADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLRGKEELKGNYLLDKIMGIETRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGASPIGTLGYVRAVGEIATQSEVKFDSIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIKEAAELLGVKVEVRPELYDYSFGEYGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGLVDLARKGELGEKILFIHTGGISGTFHYGDKLLSLL 325
                                    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     


Chain C from PDB  Type:PROTEIN  Length:325
 aligned with 1A1D_PYRHO | O57809 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:325
                                    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     
           1A1D_PYRHO     1 MHPKIFALLAKFPRVELIPWETPIQYLPNISREIGADVYIKRDDLTGLGIGGNKIRKLEYLLGDALSKGADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLRGKEELKGNYLLDKIMGIETRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGASPIGTLGYVRAVGEIATQSEVKFDSIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIKEAAELLGVKVEVRPELYDYSFGEYGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGLVDLARKGELGEKILFIHTGGISGTFHYGDKLLSLL 325
               SCOP domains d1j0ac_ C: 1-aminocyclopropane-1-carboxylate deaminase                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1j0aC01 C:1-52,C:158-325                            1j0aC02 C:53-156  [code=3.40.50.1100, no name defined]                                                  -1j0aC01 C:1-52,C:158-325  [code=3.40.50.1100, no name defined]                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.............eeehhhhhhh...eeeeee.hhh......hhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhh..eeeeeee......hhhhhhhhh..eeeee.......hhhhhhhhhhhhhhh...eeeehhhhh....hhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhhhh.......eeee.........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j0a C   1 MHPKIFALLAKFPRVELIPWETPIQYLPNISREIGADVYIKRDDLTGLGIGGNKIRKLEYLLGDALSKGADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLRGKEELKGNYLLDKIMGIETRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGASPIGTLGYVRAVGEIATQSEVKFDSIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIKEAAELLGVKVEVRPELYDYSFGEYGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGLVDLARKGELGEKILFIHTGGISGTFHYGDKLLSLL 325
                                    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
   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, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J0A)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (1A1D_PYRHO | O57809)
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:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        1A1D_PYRHO | O57809: 1j0b

(-) Related Entries Specified in the PDB File

1f2d ACC DEAMINASE FROM HANSENULA SATURNUS
1j0b ACC DEAMINASE HOMOLOGURE COMPLEXED WITH INHIITOR
1j0c ACC DEAMINASE MUTATED TO CATALYTIC RESIDUE
1j0d ACC DEAMINASE MUTANT COMPLEXED WITH ACC
1j0e ACC DEAMINASE MUTANT REACTON INTERMEDIATE