2MTA - JenaLib

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Title :   CRYSTAL STRUCTURE OF A TERNARY ELECTRON TRANSFER COMPLEX BETWEEN METHYLAMINE DEHYDROGENASE, AMICYANIN AND A C-TYPE CYTOCHROME

Authors :   L. Chen, F. S. Mathews

Date :   26 Oct 93 (Deposition) - 31 Jan 94 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,C,H,L
Biol. Unit 1: A,C,H,L  (2x)

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

Reference :   L. Chen, R. C. Durley, F. S. Mathews, V. L. Davidson
Structure Of An Electron Transfer Complex: Methylamine Dehydrogenase, Amicyanin, And Cytochrome C551I.
Science V. 264 86 1994
PubMed-ID: 8140419
(for further references see the PDB file header)

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

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

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

Molecule 4 - CYTOCHROME C551I
	Chains	:	C
	Engineered	:	YES
	Organism Scientific	:	PARACOCCUS DENITRIFICANS
	Organism Taxid	:	266

		1	2	3	4
Asymmetric Unit	:	A	C	H	L
Biological Unit 1 (2x)	:	A	C	H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 4)

No.	Name	Count	Type	Full Name
1	CU	1	Ligand/Ion	COPPER (II) ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	PO4	1	Ligand/Ion	PHOSPHATE ION
4	TRQ	1	Mod. Amino Acid	2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1H-INDOL-3-YL)-PROPIONIC ACID

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	PO4	2	Ligand/Ion	PHOSPHATE ION
4	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	LYS H:341 , HIS H:362	BINDING SITE FOR RESIDUE PO4 H 0
3	AC3	SOFTWARE	MET C:56 , CYS C:57 , CYS C:60 , HIS C:61 , PRO C:71 , TRP C:78 , THR C:79 , TYR C:80 , ASN C:83 , LEU C:89 , THR C:92 , LEU C:93 , ALA C:97 , THR C:98 , GLN C:100 , MET C:101 , MET C:104	BINDING SITE FOR RESIDUE HEM C 200
4	COP	UNKNOWN	CU A:0 , GLY H:53 , GLY H:92 , THR H:95 , VAL H:98	NULL
5	HEM	UNKNOWN	HEM C:200	NULL
6	TTQ	UNKNOWN	ARG H:57 , PRO H:108	NULL

Asymmetric Unit

No.	Residues
1	H:168	-	H:183
2	L:23	-	L:88
3	L:29	-	L:61
4	L:36	-	L:121
5	L:38	-	L:86
6	L:46	-	L:77
7	L:78	-	L:109

Asymmetric Unit

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

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

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYCL_PARDE	52-146	1	C:30-124
2	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AMCY_PARDE	111-124	1	A:85-98

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYCL_PARDE	52-146	2	C:30-124
2	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AMCY_PARDE	111-124	2	A:85-98

(no "Exon" information available for 2MTA)

Asymmetric 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:105
 aligned with AMCY_PARDE | P22364 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:105
                                    36        46        56        66        76        86        96       106       116       126     
           AMCY_PARDE    27 DKATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHPFMRGKVVVE 131
               SCOP domains d2mtaa_ A: Amicyanin                                                                                      SCOP domains
               CATH domains 2mtaA00 A:1-105 Cupredoxins -  blue copper proteins                                                       CATH domains
               Pfam domains ----------------Copper-bind-2mtaA01 A:17-105                                                              Pfam domains
         Sec.struct. author eeeeeeeeeeeee.......eeeeeee..eeeeeeeee..eeeeeeee...eeeeeee.......eeeeeeee.eeeeeeeee.eeeeeeee.....eeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------COPPER_BLUE   ------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 2mta A   1 DKATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHPFMRGKVVVE 105
                                    10        20        30        40        50        60        70        80        90       100

Chain C from PDB  Type:PROTEIN  Length:147
 aligned with CYCL_PARDE | P29899 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:147
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       
           CYCL_PARDE    23 APQFFNIIDGSPLNFDDAMEEGRDTEAVKHFLETGENVYNEDPEILPEAEELYAGMCSGCHGHYAEGKIGPGLNDAYWTYPGNETDVGLFSTLYGGATGQMGPMWGSLTLDEMLRTMAWVRHLYTGDPKDASWLTDEQKAGFTPFQP 169
               SCOP domains d2mtac_ C: Cytochrome c551                                                                                                                          SCOP domains
               CATH domains 2mtaC00 C:1-147 Cytochrome c                                                                                                                        CATH domains
               Pfam domains --------------------------------------------Cytochrome_CBB3-2mtaC01 C:45-120                                            --------------------------- Pfam domains
         Sec.struct. author ................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------CYTC  PDB: C:30-124 UniProt: 52-146                                                            ----------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2mta C   1 APQFFNIIDGSPLNFDDAMEEGRDTEAVKHFLETGENVYNEDPEILPEAEELYAGMCSGCHGHYAEGKIGPGLNDAYWTYPGNETDVGLFSTLYGGATGQMGPMWGSLTLDEMLRTMAWVRHLYTGDPKDASWLTDEQKAGFTPFQP 147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain H from PDB  Type:PROTEIN  Length:373
 aligned with DHMH_PARDE | P29894 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:373
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414   
           DHMH_PARDE    45 QGQAAARAAAADLAAGQDDEPRILEAPAPDARRVYVNDPAHFAAVTQQFVIDGEAGRVIGMIDGGFLPNPVVADDGSFIAHASTVFSRIARGERTDYVEVFDPVTLLPTADIELPDAPRFLVGTYPWMTSLTPDGKTLLFYQFSPAPAVGVVDLEGKAFKRMLDVPDCYHIFPTAPDTFFMHCRDGSLAKVAFGTEGTPEITHTEVFHPEDEFLINHPAYSQKAGRLVWPTYTGKIHQIDLSSGDAKFLPAVEALTEAERADGWRPGGWQQVAYHRALDRIYLLVDQRDEWRHKTASRLLVVLDAKTGERLAKFEMGHEIDSINVSQDEKPLLYALSTGDKTLYIHDAESGEELRSVNQLGHGPQVITTADMG 417
               SCOP domains d2mtah_ H: Methylamine dehydrogenase, H-chain                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2mtaH00 H:1-373 YVTN repeat-like/Quinoprotein amine dehydrogenase                                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains -----------------------------Me-amine-dh_H-2mtaH01 H:30-371                                                                                                                                                                                                                                                                                                                        -- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...............eeeeeeee.....eeeeeeeee..eeeeeeeeee.eeeeeee....eeeeeeeeeee...eeeeeeeeeee...eeeeeeeeee.......eeee.eeeeee..eeeeeeeee.eeeeeeeee.eeeeeeeee...eeeeeeee.eeeeeeee.eeeeeeeee..eeeeeeeeee......eeeeeeeeee..eeeeeeee.eeeeeeeee..eeeeeeeee..hhhhhhhh.......eeeeee..eeeeeeeeee....eeeeeeeeeeeee..eeeeeeeeee....eeeeeee.eeeeeeeee..eeeeeeee..eeeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2mta H   1 QGQAAARAAAADLAAGQDDEPRILEAPAPDARRVYVNDPAHFAAVTQQFVIDGEAGRVIGMIDGGFLPNPVVADDGSFIAHASTVFSRIARGERTDYVEVFDPVTLLPTADIELPDAPRFLVGTYPWMTSLTPDGKTLLFYQFSPAPAVGVVDLEGKAFKRMLDVPDCYHIFPTAPDTFFMHCRDGSLAKVAFGTEGTPEITHTEVFHPEDEFLINHPAYSQKAGRLVWPTYTGKIHQIDLSSGDAKFLPAVEALTEAERADGWRPGGWQQVAYHRALDRIYLLVDQRDEWRHKTASRFLVVLDAKTGERLAKFEMGHEIDSINVSQDEKPLLYALSTGDKTLYIHDAESGEELRSVNQLGHGPQVITTADMG 373
                                    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       370

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 d2mtal_ L: Methylamine dehydrogenase                                                                                          SCOP domains
               CATH domains 2mtaL00 L:7-131 Electron Transport Ethylamine Dehydrogenase                                                                   CATH domains
               Pfam domains -Me-amine-dh_L-2mtaL01 L:8-130                                                                                              - Pfam domains
         Sec.struct. author .......................eeeeee....eee..eee..eeeeeeeeeeeeeee...eeeeeeeeeee.......eeeee............................eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2mta L   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 '\|'

Asymmetric Unit(hide GO term definitions)

Chain A (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).

Chain C (CYCL_PARDE | P29899)

molecular function
	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:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0015945	methanol metabolic process	The chemical reactions and pathways involving methanol, CH3-OH, a colorless, flammable, mobile, poisonous liquid, widely used as a solvent.
	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 H (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 (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 Unit
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	Cis Peptide Bonds
		Ser H:144 - Pro H:145	[ RasMol ]

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 4)

Sites (6, 6)

SS Bonds (7, 7)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

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SCOP Domains (4, 4)

CATH Domains (4, 4)

Pfam Domains (4, 4)

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