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Title :   CRYSTAL STRUCTURE OF AN ELECTRON-TRANSFER COMPLEX BETWEEN METHYLAMINE DEHYDROGENASE AND AMICYANIN

Authors :   L. Chen, R. Durley, F. S. Mathews

Date :   02 Mar 92 (Deposition) - 31 Oct 93 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

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

Reference :   L. Chen, R. Durley, B. J. Poliks, K. Hamada, Z. Chen, F. S. Mathews, V. L. Davidson, Y. Satow, E. Huizinga, F. M. Vellieux, W. G. J. Hol
Crystal Structure Of An Electron-Transfer Complex Between Methylamine Dehydrogenase And Amicyanin.
Biochemistry V. 31 4959 1992
PubMed-ID: 1599920 | Reference-DOI: 10.1021/BI00136A006
(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

Molecule 3 - AMICYANIN
	Chains	:	A, B
	Engineered	:	YES
	Organism Scientific	:	PARACOCCUS DENITRIFICANS
	Organism Taxid	:	266

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	H	J	L	M

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CU	2	Ligand/Ion	COPPER (II) ION
2	TRQ	2	Mod. Amino Acid	2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1H-INDOL-3-YL)-PROPIONIC ACID

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:53 , CYS A:92 , HIS A:95 , MET A:98	BINDING SITE FOR RESIDUE CU A 0
2	AC2	SOFTWARE	HIS B:53 , CYS B:92 , HIS B:95 , MET B:98	BINDING SITE FOR RESIDUE CU B 0
3	CUE	UNKNOWN	CU A:0 , HIS A:53 , CYS A:92 , HIS A:95 , MET A:98	NULL
4	CUF	UNKNOWN	CU B:0 , HIS B:53 , CYS B:92 , HIS B:95 , MET B:98	NULL
5	TQB	UNKNOWN	TRQ L:57 , TRP L:107	NULL
6	TQD	UNKNOWN	TRQ M:57 , TRP M:107	NULL

Asymmetric/Biological Unit

No.	Residues
1	L:23	-	L:88
2	L:29	-	L:61
3	L:36	-	L:119
4	L:38	-	L:86
5	L:46	-	L:77
6	L:78	-	L:108
7	M:23	-	M:88
8	M:29	-	M:61
9	M:36	-	M:119
10	M:38	-	M:86
11	M:46	-	M:77
12	M:78	-	M:108

Asymmetric/Biological Unit

No.	Residues
1	Ile A:5	-	Pro A:6
2	Ile B:5	-	Pro B:6

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AMCY_PARDE	111-124	2	A:85-98 B:85-98

(no "Exon" information available for 1MDA)

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:103
 aligned with AMCY_PARDE | P22364 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:103
                                    38        48        58        68        78        88        98       108       118       128   
           AMCY_PARDE    29 ATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHPFMRGKVVVE 131
               SCOP domains d1mdaa_ A: Amicyanin                                                                                    SCOP domains
               CATH domains 1mdaA00 A:3-105 Cupredoxins -  blue copper proteins                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeeeeeeee.......eeeeeee..eeeeeeeee..eeeeeeee...eeeeeee.......eeeeeeee.eeeeeeeee.eeeeeeee.....eeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------COPPER_BLUE   ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1mda A   3 ATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHPFMRGKVVVE 105
                                    12        22        32        42        52        62        72        82        92       102

Chain B from PDB  Type:PROTEIN  Length:103
 aligned with AMCY_PARDE | P22364 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:103
                                    38        48        58        68        78        88        98       108       118       128   
           AMCY_PARDE    29 ATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHPFMRGKVVVE 131
               SCOP domains d1mdab_ B: Amicyanin                                                                                    SCOP domains
               CATH domains 1mdaB00 B:3-105 Cupredoxins -  blue copper proteins                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeeeeeeee.......eeeeeee..eeeeeeeee..eeeeeeee...eeeeeee.......eeeeeeee.eeeeeeeee.eeeeeeee.....eeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------COPPER_BLUE   ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1mda B   3 ATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHPFMRGKVVVE 105
                                    12        22        32        42        52        62        72        82        92       102

Chain H from PDB  Type:PROTEIN  Length:368
                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d1mdah_ H: Methylamine dehydrogenase, H-chain                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1mdaH00 H:1-368 YVTN repeat-like/Quinoprotein amine dehydrogenase                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...............eeeeeeee.....eeeeeeeee..eeeeeeeeee.eeeeeee....eeeeeeeeeee...eeeeeeeeeee....eeeeeeee........eeee.eeeeee..eeeeeeeeee.eeeeeeeee.eeeeeeeee.eeeeeeee.eeeeeeee.eeeeeeeee..eeeeeee...........eeeeeee..eeeeee...eeeeeeee..eeeeeeeee...hhhhhhhh......eeeeee..eeeeeeee.......eeeeeeeeeeeee.eeeeeeeee.eeeeeeeeeeee.eeeeeeeeee.eeeeeeee.eeeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mda H   1 EKSKVAGSAAAASAAAASDGSSCDHGPGAISRRSHITLPAYFAGTTENWVSCAGCGVTLGHSLGAFLSLAVAGHSGSDFALASTSFARSAKGKRTDYVEVFDPVTFLPIADIELPDAPRFSVGPRVHIIGNCASSACLLFFLFGSSAAAGLSVPGASDDQLTKSASCFHIHPGAAATHYLGSCPASLAASDLAAAPAAAGIVGAQCTGAQNCSSQAAQANYPGMLVWAVASSILQGDIPAAGATMKAAIDGNESGRKADNFRSAGFQMVAKLKNTDGIMILTVEHSRSCLAAAENTSSVTASVGQTSGPISNGHDSDAIIAAQDGASDNYANSAGTEVLDIYDAASDQDQSSVELDKGPESLSVQNEA 368
                                    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       330       340       350       360

Chain J from PDB  Type:PROTEIN  Length:368
                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d1mdaj_ J: Methylamine dehydrogenase, H-chain                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1mdaJ00 J:1-368 YVTN repeat-like/Quinoprotein amine dehydrogenase                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...............eeeeeeee.....eeeeeeeee..eeeeeeeeee.eeeeeee....eeeeeeeeeee...eeeeeeeeeee....eeeeeeee........eeee.eeeeee..eeeeeeeeee.eeeeeeeee.eeeeeeeee.eeeeeeee.eeeeeeee.eeeeeeeee..eeeeeee...........eeeeeee..eeeeee..........e..eeeeeeeee...hhhhhhhh......eeeeee..eeeeeeee.......eeeeeeeeeeeee.eeeeeeeee.eeeeeeeeeeee.eeeeeeeeee.eeeeeeee.eeeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mda J   1 EKSKVAGSAAAASAAAASDGSSCDHGPGAISRRSHITLPAYFAGTTENWVSCAGCGVTLGHSLGAFLSLAVAGHSGSDFALASTSFARSAKGKRTDYVEVFDPVTFLPIADIELPDAPRFSVGPRVHIIGNCASSACLLFFLFGSSAAAGLSVPGASDDQLTKSASCFHIHPGAAATHYLGSCPASLAASDLAAAPAAAGIVGAQCTGAQNCSSQAAQANYPGMLVWAVASSILQGDIPAAGATMKAAIDGNESGRKADNFRSAGFQMVAKLKNTDGIMILTVEHSRSCLAAAENTSSVTASVGQTSGPISNGHDSDAIIAAQDGASDNYANSAGTEVLDIYDAASDQDQSSVELDKGPESLSVQNEA 368
                                    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       330       340       350       360

Chain L from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains d1mdal_ L: Methylamine dehydrogenase                                                                                      SCOP domains
               CATH domains 1mdaL00 L:7-127 Electron Transport Ethylamine Dehydrogenase                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................eeeeee....eee..eee..eeeeeeeeeeeeeee...eeeeeeeeeee.......eeeee...........................eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mda L   7 VDPRAKWQPQDNDIQACDYWRHCSIAGNICDCSAGSLTSCPPGTLVASGSwVGSCYNPPDPNKYITAYRDCCGYNVSGRCACLNTEGELPVYNKDANDIIWCFGGEDGMTYHCSISPVSGA 127
                                    16        26        36        46        56|       66        76        86        96       106       116       126 
                                                                             57-TRQ

Chain M from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains d1mdam_ M: Methylamine dehydrogenase                                                                                      SCOP domains
               CATH domains 1mdaM00 M:7-127 Electron Transport Ethylamine Dehydrogenase                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................eeeeee....eee..eee..eeeeeeeeeeeeeee...eeeeeeeeeee.......eeeee...........................eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mda M   7 VDPRAKWQPQDNDIQACDYWRHCSIAGNICDCSAGSLTSCPPGTLVASGSwVGSCYNPPDPNKYITAYRDCCGYNVSGRCACLNTEGELPVYNKDANDIIWCFGGEDGMTYHCSISPVSGA 127
                                    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 1MDA)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (AMCY_PARDE | P22364)

molecular function
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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).

Asymmetric/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (6, 6)

SS Bonds (12, 12)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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