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(-) Description

Title :  CRYSTAL STRUCTURE OF AROMATIC AMINE DEHYDROGENASE TTQ-PHENYLACETALDEHYDE ADDUCT OXIDIZED WITH FERRICYANIDE
 
Authors :  A. Roujeinikova, D. Leys
Date :  16 Jan 07  (Deposition) - 01 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A,B,D,H
Keywords :  Oxidoreductase, Ttq (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Roujeinikova, P. Hothi, L. Masgrau, M. J. Sutcliffe, N. S. Scrutton D. Leys
New Insights Into The Reductive Half-Reaction Mechanism Of Aromatic Amine Dehydrogenase Revealed By Reaction With Carbinolamine Substrates.
J. Biol. Chem. V. 282 23766 2007
PubMed-ID: 17475620  |  Reference-DOI: 10.1074/JBC.M700677200

(-) Compounds

Molecule 1 - AROMATIC AMINE DEHYDROGENASE, SMALL SUBUNIT
    Chains: D, H
    EC Number: 1.4.99.4
    Organism Scientific: ALCALIGENES FAECALIS
    Organism Taxid: 511
 
Molecule 2 - AROMATIC AMINE DEHYDROGENASE, LARGE SUBUNIT
    Chains: A, B
    EC Number: 1.4.99.4
    Organism Scientific: ALCALIGENES FAECALIS
    Organism Taxid: 511

 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
1HY12Ligand/IonPHENYLACETALDEHYDE
2TQQ2Mod. Amino Acid(S)-2-AMINO-3-(6,7-DIHYDRO-6-IMINO-7-OXO-1H-INDOL-3-YL)PROPANOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU B:179 , ASP D:84 , TQQ D:109 , ASP D:128 , VAL D:158 , ASN D:159 , TRP D:160 , PHE D:169BINDING SITE FOR RESIDUE HY1 D 2002
2AC2SOFTWAREASP H:84 , TQQ H:109 , ASP H:128 , VAL H:158 , ASN H:159 , TRP H:160 , PHE H:169BINDING SITE FOR RESIDUE HY1 H 2001

(-) 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 2OK4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OK4)

(-) Exons   (0, 0)

(no "Exon" information available for 2OK4)

(-) 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
                                    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       350       360       370       380       390
           AAUB_ALCFA    31 EVLTGGHSVSAPQENRIYVMDSVFMHLTESRVHVYDYTNGKFLGMVPTAFNGHVQVSNDGKKIYTMTTYHERITRGKRSDVVEVWDADKLTFEKEISLPPKRVQGLNYDGLFRQTTDGKFIVLQNASPATSIGIVDVAKGDYVEDVTAAAGCWSVIPQPNRPRSFMTICGDGGLLTINLGEDGKVASQSRSKQMFSVKDDPIFIAPALDKDKAHFVSYYGNVYSADFSGDEVKVDGPWSLLNDEDKAKNWVPGGYNLVGLHRASGRMYVFMHPDGKEGTHKFPAAEIWVMDTKTKQRVARIPGRDALSMTIDQQRNLMLTLDGGNVNVYDISQPEPKLLRTIEGAAEASLQVQFHPVGGV 390
               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
                 2ok4 A  74 EVLTGGHSVSAPQENRIYVMDSVFMHLTESRVHVYDYTNGKFLGMVPTAFNGHVQVSNDGKKIYTMTTYHERITRGKRSDVVEVWDADKLTFEKEISLPPKRVQGLNYDGLFRQTTDGKFIVLQNASPATSIGIVDVAKGDYVEDVTAAAGCWSVIPQPNRPRSFMTICGDGGLLTINLGEDGKVASQSRSKQMFSVKDDPIFIAPALDKDKAHFVSYYGNVYSADFSGDEVKVDGPWSLLNDEDKAKNWVPGGYNLVGLHRASGRMYVFMHPDGKEGTHKFPAAEIWVMDTKTKQRVARIPGRDALSMTIDQQRNLMLTLDGGNVNVYDISQPEPKLLRTIEGAAEASLQVQFHPVGGT 433
                                    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433


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 (1) -------------Me-amine-dh_H-2ok4B01 B:86-424                                                                                                                                                                                                                                                                                                                     --------- Pfam domains (1)
           Pfam domains (2) -------------Me-amine-dh_H-2ok4B02 B:86-424                                                                                                                                                                                                                                                                                                                     --------- Pfam domains (2)
         Sec.struct. author ............hhh.eeeeee.hhhhhhh.eeeeee.....eeeeee..eeeeeee.....eeeeeeeee.......eeeeeeeee.....eeeeeee.........hhh.eee.....eeeeeee...eeeeeee....ee...hhhhh.eeeeee......eeeeee....eeeeee.....eeeeee................ee...eeeee....eeeeee......eeeeeee..hhhhhhh..ee.....eeee....eeeeeee.............eeeeee....eeeeeee.....eeeee....eeeee....eeeee......eeeeee......eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ok4 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:110
 aligned with AAUA_ALCFA | P84887 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:110
                                    80        90       100       110       120       130       140       150       160       170       180
           AAUA_ALCFA    71 EVNSCDYWRHCAVDGFLCSCCGGTTTTCPPGSTPSPISWIGTCHNPHDGKDYLISYHDCCGKTACGRCQCNTQTRERPGYEFFLHNDVNWCMANENSTFHCTTSVLVGLA 180
               SCOP domains d2ok4d_ D: automated matches                                                                                   SCOP domains
               CATH domains 2ok4D00 D:71-180 Electron Transport Ethylamine Dehydrogenase                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh..eee.hhhh...........ee......eeee......eeeee..eee........eee......hhhhhhhh.............eeee..eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 2ok4 D  71 EVNSCDYWRHCAVDGFLCSCCGGTTTTCPPGSTPSPISwIGTCHNPHDGKDYLISYHDCCGKTACGRCQCNTQTRERPGYEFFLHNDVNWCMANENSTFHCTTSVLVGLA 180
                                    80        90       100       110       120       130       140       150       160       170       180
                                                                109-TQQ                                                                   


Chain H from PDB  Type:PROTEIN  Length:122
 aligned with AAUA_ALCFA | P84887 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:122
                                    68        78        88        98       108       118       128       138       148       158       168       178  
           AAUA_ALCFA    59 HISLNPDLANEDEVNSCDYWRHCAVDGFLCSCCGGTTTTCPPGSTPSPISWIGTCHNPHDGKDYLISYHDCCGKTACGRCQCNTQTRERPGYEFFLHNDVNWCMANENSTFHCTTSVLVGLA 180
               SCOP domains d2ok4h_ H: automated matches                                                                                               SCOP domains
               CATH domains 2ok4H00 H:59-180 Electron Transport Ethylamine Dehydrogenase                                                               CATH domains
           Pfam domains (1) ----Me-amine-dh_L-2ok4H01 H:63-180                                                                                         Pfam domains (1)
           Pfam domains (2) ----Me-amine-dh_L-2ok4H02 H:63-180                                                                                         Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhh...hhhhh..eee.hhhh...........ee......eeee......eeeee..eee........eee......hhhhhhhh.............eeee..eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ok4 H  59 HISLNPDLANEDEVNSCDYWRHCAVDGFLCSCCGGTTTTCPPGSTPSPISwIGTCHNPHDGKDYLISYHDCCGKTACGRCQCNTQTRERPGYEFFLHNDVNWCMANENSTFHCTTSVLVGLA 180
                                    68        78        88        98       108|      118       128       138       148       158       168       178  
                                                                            109-TQQ
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Beta_propeller (192)
(-)
Clan: no clan defined [family: Me-amine-dh_L] (16)

(-) 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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  2ok4
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  AAUA_ALCFA | P84887
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  AAUB_ALCFA | P84888
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2OK4)