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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SCHIFF BASE INTERMEDIATE IN THE REDUCTIVE HALF-REACTION OF AROMATIC AMINE DEHYDROGENASE (AADH) WITH TRYPTAMINE. MONOCLINIC FORM
 
Authors :  L. Masgrau, A. Roujeinikova, L. O. Johannissen, P. Hothi, J. Basran, K. E. Ranaghan, A. J. Mulholland, M. J. Sutcliffe, N. S. Scrutton, D. Le
Date :  27 Jul 05  (Deposition) - 25 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  A,B,D,H
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Masgrau, A. Roujeinikova, L. O. Johannissen, P. Hothi, J. Basran, K. E. Ranaghan, A. J. Mulholland, M. J. Sutcliffe, N. S. Scrutton, D. Leys
Atomic Description Of An Enzyme Reaction Dominated By Proto Tunneling
Science V. 312 237 2006
PubMed-ID: 16614214  |  Reference-DOI: 10.1126/SCIENCE.1126002

(-) Compounds

Molecule 1 - AROMATIC AMINE DEHYDROGENASE
    Chains: D, H
    EC Number: 1.4.99.4
    Fragment: RESIDUES 48-182
    Organism Scientific: ALCALIGENES FAECALIS
    Organism Taxid: 511
    Strain: IFO 14479
 
Molecule 2 - AROMATIC AMINE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.4.99.4
    Fragment: RESIDUES 73-433
    Organism Scientific: ALCALIGENES FAECALIS
    Organism Taxid: 511
    Strain: IFO 14479

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABDH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1TRQ2Mod. Amino Acid2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1H-INDOL-3-YL)-PROPIONIC ACID
2TSH2Ligand/Ion2-(1H-INDOL-3-YL)ETHANIMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:100 , GLY A:178 , LEU A:179 , ASP H:84 , TRQ H:109 , ASP H:128 , ASN H:156 , VAL H:158 , ASN H:159 , THR H:172BINDING SITE FOR RESIDUE TSH H 1
2AC2SOFTWARELEU B:100 , GLY B:178 , LEU B:179 , ASP D:84 , TRQ D:109 , ASP D:128 , ASN D:156 , VAL D:158 , ASN D:159 , THR D:172BINDING SITE FOR RESIDUE TSH D 2

(-) SS Bonds  (16, 16)

Asymmetric/Biological Unit
No.Residues
1A:225 -A:242
2B:225 -B:242
3D:75 -D:140
4D:81 -D:113
5D:88 -D:171
6D:90 -D:138
7D:91 -D:135
8D:98 -D:129
9D:130 -D:161
10H:75 -H:140
11H:81 -H:113
12H:88 -H:171
13H:90 -H:138
14H:91 -H:135
15H:98 -H:129
16H:130 -H:161

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser A:200 -Pro A:201
2Gly A:309 -Pro A:310
3Ser B:200 -Pro B:201
4Gly B:309 -Pro B:310

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2AGY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2AGY)

(-) Exons   (0, 0)

(no "Exon" information available for 2AGY)

(-) Sequences/Alignments

Asymmetric/Biological 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:360
 aligned with AAUB_ALCFA | P84888 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:360
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389
           AAUB_ALCFA    30 REVLTGGHSVSAPQENRIYVMDSVFMHLTESRVHVYDYTNGKFLGMVPTAFNGHVQVSNDGKKIYTMTTYHERITRGKRSDVVEVWDADKLTFEKEISLPPKRVQGLNYDGLFRQTTDGKFIVLQNASPATSIGIVDVAKGDYVEDVTAAAGCWSVIPQPNRPRSFMTICGDGGLLTINLGEDGKVASQSRSKQMFSVKDDPIFIAPALDKDKAHFVSYYGNVYSADFSGDEVKVDGPWSLLNDEDKAKNWVPGGYNLVGLHRASGRMYVFMHPDGKEGTHKFPAAEIWVMDTKTKQRVARIPGRDALSMTIDQQRNLMLTLDGGNVNVYDISQPEPKLLRTIEGAAEASLQVQFHPVGG 389
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhh.eeeeee.hhhhhhh.eeeeee.....eeeeee..eeeeeee.....eeeeeeeee.......eeeeeeeee.....eeeeeee.........hhh.eee.....eeeeeee...eeeeeee....eeeeeehhhh.eeeeee......eeeeee....eeeeee.....eeeeee................ee...eeeee....eeeeee......eeeeeee..hhhhhhh..ee.....eeee....eeeeeee.............eeeeee....eeeeeee.....eeeee....eeeee....eeeee......eeeeee........eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2agy A  73 REVLTGGHSVSAPQENRIYVMDSVFMHLTESRVHVYDYTNGKFLGMVPTAFNGHVQVSNDGKKIYTMTTYHERITRGKRSDVVEVWDADKLTFEKEISLPPKRVQGLNYDGLFRQTTDGKFIVLQNASPATSIGIVDVAKGDYVEDVTAAAGCWSVIPQPNRPRSFMTICGDGGLLTINLGEDGKVASQSRSKQMFSVKDDPIFIAPALDKDKAHFVSYYGNVYSADFSGDEVKVDGPWSLLNDEDKAKNWVPGGYNLVGLHRASGRMYVFMHPDGKEGTHKFPAAEIWVMDTKTKQRVARIPGRDALSMTIDQQRNLMLTLDGGNVNVYDISQPEPKLLRTIEGAAEASLQVQFHPVGG 432
                                    82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432


Chain B from PDB  Type:PROTEIN  Length:361
 aligned with AAUB_ALCFA | P84888 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:361
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389 
           AAUB_ALCFA    30 REVLTGGHSVSAPQENRIYVMDSVFMHLTESRVHVYDYTNGKFLGMVPTAFNGHVQVSNDGKKIYTMTTYHERITRGKRSDVVEVWDADKLTFEKEISLPPKRVQGLNYDGLFRQTTDGKFIVLQNASPATSIGIVDVAKGDYVEDVTAAAGCWSVIPQPNRPRSFMTICGDGGLLTINLGEDGKVASQSRSKQMFSVKDDPIFIAPALDKDKAHFVSYYGNVYSADFSGDEVKVDGPWSLLNDEDKAKNWVPGGYNLVGLHRASGRMYVFMHPDGKEGTHKFPAAEIWVMDTKTKQRVARIPGRDALSMTIDQQRNLMLTLDGGNVNVYDISQPEPKLLRTIEGAAEASLQVQFHPVGGV 390
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhh.eeeeee.hhhhhhh.eeeeee.....eeeeee..eeeeeee.....eeeeeeeee.......eeeeeeeee....eeeeeeee.........hhh.eee.....eeeeeee...eeeeeee....ee...hhhhh.eeeeee......eeeeee....eeeeee.....eeeeee................ee...eeeee....eeeeee......eeeeeee..hhhhhhh..ee.....eeee....eeeeeee.............eeeeee....eeeeeee.....eeeee....eeeee....eeeee......eeeeee........eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2agy B  73 REVLTGGHSVSAPQENRIYVMDSVFMHLTESRVHVYDYTNGKFLGMVPTAFNGHVQVSNDGKKIYTMTTYHERITRGKRSDVVEVWDADKLTFEKEISLPPKRVQGLNYDGLFRQTTDGKFIVLQNASPATSIGIVDVAKGDYVEDVTAAAGCWSVIPQPNRPRSFMTICGDGGLLTINLGEDGKVASQSRSKQMFSVKDDPIFIAPALDKDKAHFVSYYGNVYSADFSGDEVKVDGPWSLLNDEDKAKNWVPGGYNLVGLHRASGRMYVFMHPDGKEGTHKFPAAEIWVMDTKTKQRVARIPGRDALSMTIDQQRNLMLTLDGGNVNVYDISQPEPKLLRTIEGAAEASLQVQFHPVGGT 433
                                    82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432 


Chain D from PDB  Type:PROTEIN  Length:109
 aligned with AAUA_ALCFA | P84887 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:109
                                    80        90       100       110       120       130       140       150       160       170         
           AAUA_ALCFA    71 EVNSCDYWRHCAVDGFLCSCCGGTTTTCPPGSTPSPISWIGTCHNPHDGKDYLISYHDCCGKTACGRCQCNTQTRERPGYEFFLHNDVNWCMANENSTFHCTTSVLVGL 179
               SCOP domains d2agyd_ D: automated matches                                                                                  SCOP domains
               CATH domains 2agyD00 D:71-179 Electron Transport Ethylamine Dehydrogenase                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh..eee.hhhh...........ee....eeeeee......eeeeee.eee........eee......hhhhhhhh.............eeee..eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 2agy D  71 EVNSCDYWRHCAVDGFLCSCCGGTTTTCPPGSTPSPISwIGTCHNPHDGKDYLISYHDCCGKTACGRCQCNTQTRERPGYEFFLHNDVNWCMANENSTFHCTTSVLVGL 179
                                    80        90       100       110       120       130       140       150       160       170         
                                                                109-TRQ                                                                  


Chain H from PDB  Type:PROTEIN  Length:105
 aligned with AAUA_ALCFA | P84887 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:109
                                    80        90       100       110       120       130       140       150       160       170         
           AAUA_ALCFA    71 EVNSCDYWRHCAVDGFLCSCCGGTTTTCPPGSTPSPISWIGTCHNPHDGKDYLISYHDCCGKTACGRCQCNTQTRERPGYEFFLHNDVNWCMANENSTFHCTTSVLVGL 179
               SCOP domains d2agyh_ H: automated matches                                                                                  SCOP domains
               CATH domains 2agyH00 H:71-179 Electron Transport Ethylamine     Dehydrogenase                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh..eee.hhhh...........ee....eeeee...----.eeeee.eee........eee.........hhhhh.............eeee..eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 2agy H  71 EVNSCDYWRHCAVDGFLCSCCGGTTTTCPPGSTPSPISwIGTCHNP----DYLISYHDCCGKTACGRCQCNTQTRERPGYEFFLHNDVNWCMANENSTFHCTTSVLVGL 179
                                    80        90       100       110     |   -|      130       140       150       160       170         
                                                                109-TRQ116  121
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AGY)

(-) Gene Ontology  (7, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (AAUB_ALCFA | P84888)
molecular function
    GO:0030058    amine dehydrogenase activity    Catalysis of the reaction: R-CH2-NH2 + H2O + acceptor = R-CHO + NH3 + reduced acceptor.
    GO:0030059    aralkylamine dehydrogenase (azurin) activity    Catalysis of the reaction: H(2)O + arCH(2)NH(2) + 2 azurin = 2 reduced azurin + ArCHO + NH(3). The symbol arCH(2)NH(2) represents an aralkylamine and ArCHO is an aryl aldehyde.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain D,H   (AAUA_ALCFA | P84887)
molecular function
    GO:0030058    amine dehydrogenase activity    Catalysis of the reaction: R-CH2-NH2 + H2O + acceptor = R-CHO + NH3 + reduced acceptor.
    GO:0030059    aralkylamine dehydrogenase (azurin) activity    Catalysis of the reaction: H(2)O + arCH(2)NH(2) + 2 azurin = 2 reduced azurin + ArCHO + NH(3). The symbol arCH(2)NH(2) represents an aralkylamine and ArCHO is an aryl aldehyde.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016638    oxidoreductase activity, acting on the CH-NH2 group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH2 group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
    GO:0009308    amine metabolic process    The chemical reactions and pathways involving 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.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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  2agy
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  AAUA_ALCFA | P84887
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  AAUB_ALCFA | P84888
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  1.4.99.4
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 Related Entries

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

UniProtKB/Swiss-Prot
        AAUA_ALCFA | P84887: 2agl 2agw 2agx 2agz 2ah0 2ah1 2h3x 2h47 2hj4 2hjb 2hkm 2hkr 2hxc 2i0r 2i0s 2i0t 2iaa 2iup 2iuq 2iur 2iuv 2oiz 2ojy 2ok4 2ok6 2q7q
        AAUB_ALCFA | P84888: 2agl 2agw 2agx 2agz 2ah0 2ah1 2h3x 2h47 2hj4 2hjb 2hkm 2hkr 2hxc 2i0r 2i0s 2i0t 2iaa 2iup 2iuq 2iur 2iuv 2oiz 2ojy 2ok4 2ok6 2q7q

(-) Related Entries Specified in the PDB File

2agl 2agu 2agw 2agx 2agz 2ah0 2ah1