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Title :   CRYSTAL STRUCTURE OF THE QUINOPROTEIN METHYLAMINE DEHYDROGENASE FROM PARACOCCUS DENITRIFICANS AT 1.75 ANGSTROMS

Authors :   L. Chen, F. S. Mathews

Date :   17 Dec 93 (Deposition) - 31 Jan 94 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym./Biol. Unit : H,J,L,M

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

Reference :   L. Chen, M. Doi, R. C. Durley, A. Y. Chistoserdov, M. E. Lidstrom, V. L. Davidson, F. S. Mathews
Refined Crystal Structure Of Methylamine Dehydrogenase From Paracoccus Denitrificans At 1. 75 A Resolution.
J. Mol. Biol. V. 276 131 1998
PubMed-ID: 9514722 | Reference-DOI: 10.1006/JMBI.1997.1511
(for further references see the PDB file header)

Molecule 1 - METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)
	Chains	:	H, J
	EC Number	:	1.4.99.3
	Engineered	:	YES
	Organism Scientific	:	PARACOCCUS DENITRIFICANS
	Organism Taxid	:	266

Molecule 2 - METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)
	Chains	:	L, M
	EC Number	:	1.4.99.3
	Engineered	:	YES
	Organism Scientific	:	PARACOCCUS DENITRIFICANS
	Organism Taxid	:	266

		1	2	3	4
Asymmetric/Biological Unit	:	H	J	L	M

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

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

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	TQL	UNKNOWN	TRQ L:57 , TRP L:108	NULL
2	TQM	UNKNOWN	TRQ M:57 , TRP M:108	NULL

Asymmetric/Biological Unit

No.	Residues
1	H:168	-	H:183
2	J:168	-	J:183
3	L:23	-	L:88
4	L:29	-	L:61
5	L:36	-	L:121
6	L:38	-	L:86
7	L:46	-	L:77
8	L:78	-	L:109
9	M:23	-	M:88
10	M:29	-	M:61
11	M:36	-	M:121
12	M:38	-	M:86
13	M:46	-	M:77
14	M:78	-	M:109

Asymmetric/Biological Unit

No.	Residues
1	Ser H:144	-	Pro H:145
2	Ser J:144	-	Pro J:145

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

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

(no "Exon" information available for 2BBK)

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 H from PDB  Type:PROTEIN  Length:355
 aligned with DHMH_PARDE | P29894 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:355
                                    72        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     
           DHMH_PARDE    63 DEPRILEAPAPDARRVYVNDPAHFAAVTQQFVIDGEAGRVIGMIDGGFLPNPVVADDGSFIAHASTVFSRIARGERTDYVEVFDPVTLLPTADIELPDAPRFLVGTYPWMTSLTPDGKTLLFYQFSPAPAVGVVDLEGKAFKRMLDVPDCYHIFPTAPDTFFMHCRDGSLAKVAFGTEGTPEITHTEVFHPEDEFLINHPAYSQKAGRLVWPTYTGKIHQIDLSSGDAKFLPAVEALTEAERADGWRPGGWQQVAYHRALDRIYLLVDQRDEWRHKTASRLLVVLDAKTGERLAKFEMGHEIDSINVSQDEKPLLYALSTGDKTLYIHDAESGEELRSVNQLGHGPQVITTADMG 417
               SCOP domains d2bbkh_ H: Methylamine dehydrogenase, H-chain                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2bbkH00 H:19-373 YVTN repeat-like/Quinoprotein amine dehydrogenase                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeeee.....eeeeeeee..eeeeeeeeee.eeeeeee...eeeeeeeeeee....eeeeeeeeeee....eeeeeeee..eeeeeee....eeeeee..eeeeeeee...eeeeeeeee.eeeeeeeeee.eeeeeee..eeeeeee..eeeeeeeee..eeeeeeeee.....eeeeeeeeeee..eeeeeeee..eeeeeeeee.eeeeeeeeeee.hhhhhhhh.......eeeeee..eeeeee...........eeeeeeeee..eeeeeeeeeeeee.eeeeeeee.eeeeeeeee..eeeeeeee.eeeeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bbk H  19 DEPRILEAPAPDARRVYVNDPAHFAAVTQQFVIDGEAGRVIGMIDGGFLPNPVVADDGSFIAHASTVFSRIARGERTDYVEVFDPVTLLPTADIELPDAPRFLVGTYPWMTSLTPDGKTLLFYQFSPAPAVGVVDLEGKAFKRMLDVPDCYHIFPTAPDTFFMHCRDGSLAKVAFGTEGTPEITHTEVFHPEDEFLINHPAYSQKAGRLVWPTYTGKIHQIDLSSGDAKFLPAVEALTEAERADGWRPGGWQQVAYHRALDRIYLLVDQRDEWRHKTASRFVVVLDAKTGERLAKFEMGHEIDSINVSQDEKPLLYALSTGDKTLYIHDAESGEELRSVNQLGHGPQVITTADMG 373
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368

Chain J from PDB  Type:PROTEIN  Length:355
 aligned with DHMH_PARDE | P29894 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:355
                                    72        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     
           DHMH_PARDE    63 DEPRILEAPAPDARRVYVNDPAHFAAVTQQFVIDGEAGRVIGMIDGGFLPNPVVADDGSFIAHASTVFSRIARGERTDYVEVFDPVTLLPTADIELPDAPRFLVGTYPWMTSLTPDGKTLLFYQFSPAPAVGVVDLEGKAFKRMLDVPDCYHIFPTAPDTFFMHCRDGSLAKVAFGTEGTPEITHTEVFHPEDEFLINHPAYSQKAGRLVWPTYTGKIHQIDLSSGDAKFLPAVEALTEAERADGWRPGGWQQVAYHRALDRIYLLVDQRDEWRHKTASRLLVVLDAKTGERLAKFEMGHEIDSINVSQDEKPLLYALSTGDKTLYIHDAESGEELRSVNQLGHGPQVITTADMG 417
               SCOP domains d2bbkj_ J: Methylamine dehydrogenase, H-chain                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2bbkJ00 J:19-373 YVTN repeat-like/Quinoprotein amine dehydrogenase                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeeee.....eeeeeeee..eeeeeeeeee.eeeeeee...eeeeeeeeeee....eeeeeeeeeee....eeeeeeee..eeeeeee....eeeeee..eeeeeeee...eeeeeeeee.eeeeeeeeee.eeeeeee..eeeeeee..eeeeeeeee..eeeeeeeee.....eeeeeeeeeee..eeeeeeee..eeeeeeeee.eeeeeeeeeee.hhhhhhhh.......eeeeee..eeeeee...........eeeeeeeee..eeeeeeeeeeeee.eeeeeeee.eeeeeeeee..eeeeeeee.eeeeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bbk J  19 DEPRILEAPAPDARRVYVNDPAHFAAVTQQFVIDGEAGRVIGMIDGGFLPNPVVADDGSFIAHASTVFSRIARGERTDYVEVFDPVTLLPTADIELPDAPRFLVGTYPWMTSLTPDGKTLLFYQFSPAPAVGVVDLEGKAFKRMLDVPDCYHIFPTAPDTFFMHCRDGSLAKVAFGTEGTPEITHTEVFHPEDEFLINHPAYSQKAGRLVWPTYTGKIHQIDLSSGDAKFLPAVEALTEAERADGWRPGGWQQVAYHRALDRIYLLVDQRDEWRHKTASRFVVVLDAKTGERLAKFEMGHEIDSINVSQDEKPLLYALSTGDKTLYIHDAESGEELRSVNQLGHGPQVITTADMG 373
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368

Chain L from PDB  Type:PROTEIN  Length:125
 aligned with DHML_PARDE | P22619 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:125
                                    73        83        93       103       113       123       133       143       153       163       173       183     
           DHML_PARDE    64 TDPRAKWVPQDNDIQACDYWRHCSIDGNICDCSGGSLTNCPPGTKLATASWVASCYNPTDGQSYLIAYRDCCGYNVSGRCPCLNTEGELPVYRPEFANDIIWCFGAEDDAMTYHCTISPIVGKAS 188
               SCOP domains d2bbkl_ L: Methylamine dehydrogenase                                                                                          SCOP domains
               CATH domains 2bbkL00 L:7-131 Electron Transport Ethylamine Dehydrogenase                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................eeeeee....eee..eee..eeeeeeeeeeeeeee...eeeeeeeeeee.......eeeee.............................eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bbk L   7 TDPRAKWVPQDNDIQACDYWRHCSIDGNICDCSGGSLTNCPPGTKLATASwVASCYNPTDGQSYLIAYRDCCGYNVSGRCPCLNTEGELPVYRPEFANDIIWCFGAEDDAMTYHCTISPIVGKAS 131
                                    16        26        36        46        56|       66        76        86        96       106       116       126     
                                                                             57-TRQ

Chain M from PDB  Type:PROTEIN  Length:125
 aligned with DHML_PARDE | P22619 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:125
                                    73        83        93       103       113       123       133       143       153       163       173       183     
           DHML_PARDE    64 TDPRAKWVPQDNDIQACDYWRHCSIDGNICDCSGGSLTNCPPGTKLATASWVASCYNPTDGQSYLIAYRDCCGYNVSGRCPCLNTEGELPVYRPEFANDIIWCFGAEDDAMTYHCTISPIVGKAS 188
               SCOP domains d2bbkm_ M: Methylamine dehydrogenase                                                                                          SCOP domains
               CATH domains 2bbkM00 M:7-131 Electron Transport Ethylamine Dehydrogenase                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................eeeeee....eee..eee..eeeeeeeeeeeeeee...eeeeeeeeeee.......eeeee.............................eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bbk M   7 TDPRAKWVPQDNDIQACDYWRHCSIDGNICDCSGGSLTNCPPGTKLATASwVASCYNPTDGQSYLIAYRDCCGYNVSGRCPCLNTEGELPVYRPEFANDIIWCFGAEDDAMTYHCTISPIVGKAS 131
                                    16        26        36        46        56|       66        76        86        96       106       116       126     
                                                                             57-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 '\|'

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain H,J (DHMH_PARDE | P29894)

molecular function
	GO:0030058	amine dehydrogenase activity	Catalysis of the reaction: R-CH2-NH2 + H2O + acceptor = R-CHO + NH3 + reduced acceptor.
	GO:0052876	methylamine dehydrogenase (amicyanin) activity	Catalysis of the reaction: methylamine + H2O + amicyanin = formaldehyde + ammonia + reduced amicyanin.
	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:0030416	methylamine metabolic process	The chemical reactions and pathways involving methylamine (CH3NH2).
	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 L,M (DHML_PARDE | P22619)

molecular function
	GO:0030058	amine dehydrogenase activity	Catalysis of the reaction: R-CH2-NH2 + H2O + acceptor = R-CHO + NH3 + reduced acceptor.
	GO:0052876	methylamine dehydrogenase (amicyanin) activity	Catalysis of the reaction: methylamine + H2O + amicyanin = formaldehyde + ammonia + reduced amicyanin.
	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:0030288	outer membrane-bounded periplasmic space	The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
	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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		Ser J:144 - Pro J:145	[ RasMol ]

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (14, 14)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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