2HKR - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURES OF THE CARBINOLAMINE AND SCHIFF-BASE INTERMEDIATES IN THE REDUCTIVE HALF-REACTION OF AROMATIC AMINE DEHYDROGENASE (AADH) WITH P-METHOXYPHENYLETHYLAMINE

Authors :   A. Roujeinikova, D. Leys

Date :   05 Jul 06 (Deposition) - 01 Apr 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym./Biol. Unit : A,B,D,H

Keywords :   Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Hothi, A. Roujeinikova, M. J. Sutcliffe, P. Cullis, D. Leys, N. S. Scrutton
Structure-Reactivity Correlations And Kinetic Isotope Effects In Aromatic Amine Dehydrogenase
To Be Published
PubMed: search

Molecule 1 - AROMATIC AMINE DEHYDROGENASE, SMALL SUBUNIT
	Chains	:	D, H
	EC Number	:	1.4.99.4
	Fragment	:	AADH, SMALL SUBUNIT, (RESIDUES 59-180)
	Organism Scientific	:	ALCALIGENES FAECALIS
	Organism Taxid	:	511
	Strain	:	IFO 14479

Molecule 2 - AROMATIC AMINE DEHYDROGENASE, LARGE SUBUNIT
	Chains	:	A, B
	EC Number	:	1.4.99.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	AADH, LARGE SUBUNIT, (RESIDUES 4-364)
	Gene	:	AAUB
	Organism Scientific	:	ALCALIGENES FAECALIS
	Organism Taxid	:	511

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	D	H

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	TRQ	2	Mod. Amino Acid	2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1H-INDOL-3-YL)-PROPIONIC ACID
2	ZHH	1	Ligand/Ion	2-(4-METHOXYPHENYL)ETHANAMINE
3	ZHZ	1	Ligand/Ion	2-(4-METHOXYPHENYL)ACETAMIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:124 , GLN A:177 , GLY A:178 , ASP H:84 , ASP H:128 , ASN H:159 , TRP H:160 , PHE H:169 , THR H:172	BINDING SITE FOR RESIDUE ZHZ H 1501
2	AC2	SOFTWARE	ASN B:124 , GLY B:178 , LEU B:179 , ASP D:84 , ASP D:128 , ASN D:159 , PHE D:169 , THR D:172	BINDING SITE FOR RESIDUE ZHH D 1502

Asymmetric/Biological Unit

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

Asymmetric/Biological Unit

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

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

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

(no "Exon" information available for 2HKR)

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
                 2hkr 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: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
                 2hkr B  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 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 d2hkrd_ D: automated matches                                                                                   SCOP domains
               CATH domains 2hkrD00 D:71-180 Electron Transport Ethylamine Dehydrogenase                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh..eee.hhhh...........ee....eeeeee......eeeeee.eee........eee.........hhhhh.............eeee..eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 2hkr D  71 EVNSCDYWRHCAVDGFLCSCCGGTTTTCPPGSTPSPISwIGTCHNPHDGKDYLISYHDCCGKTACGRCQCNTQTRERPGYEFFLHNDVNWCMANENSTFHCTTSVLVGLA 180
                                    80        90       100       110       120       130       140       150       160       170       180
                                                                109-TRQ

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 d2hkrh_ H: automated matches                                                                                               SCOP domains
               CATH domains 2hkrH00 H:59-180 Electron Transport Ethylamine Dehydrogenase                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh...hhhhh..eee.hhhh...........ee....eeeeeee....eeeeeee.eee........eee......hhhhhhhh.............eeee..eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hkr H  59 HISLNPDLANEDEVNSCDYWRHCAVDGFLCSCCGGTTTTCPPGSTPSPISwIGTCHNPHDGKDYLISYHDCCGKTACGRCQCNTQTRERPGYEFFLHNDVNWCMANENSTFHCTTSVLVGLA 180
                                    68        78        88        98       108|      118       128       138       148       158       168       178  
                                                                            109-TRQ

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Small proteins (3458)

Fold: Methylamine dehydrogenase, L chain (68)

Superfamily: Methylamine dehydrogenase, L chain (68)

Family: automated matches (27)

Protein domain: automated matches (27)

Alcaligenes faecalis [TaxId: 511] (27)

1a	d2hkrd_	D:
1b	d2hkrh_	H:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Electron Transport Ethylamine Dehydrogenase (43)

Homologous Superfamily: Electron Transport Ethylamine Dehydrogenase (43)

Alcaligenes faecalis. Organism_taxid: 511. Strain: ifo 14479. (17)

1a	2hkrH00	H:59-180
1b	2hkrD00	D:71-180

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

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).

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		TRQ	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZHH	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZHZ	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:309 - Pro A:310	[ RasMol ]
		Gly B:309 - Pro B:310	[ RasMol ]
		Ser A:200 - Pro A:201	[ RasMol ]
		Ser B:200 - Pro B:201	[ RasMol ]

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	2hkr
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
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	AAUA_ALCFA \| P84887
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
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	AAUB_ALCFA \| P84888
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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	1.4.99.4
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	AAUA_ALCFA \| P84887
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	AAUB_ALCFA \| P84888
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (2, 2)

SS Bonds (16, 16)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (1, 2)

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Gene Ontology (7, 12)

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