1JMX - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A QUINOHEMOPROTEIN AMINE DEHYDROGENASE FROM PSEUDOMONAS PUTIDA

Authors :   A. Satoh, I. Miyahara, K. Hirotsu

Date :   20 Jul 01 (Deposition) - 16 Jan 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,G
Biol. Unit 1: A,B,G  (1x)
Biol. Unit 2: A,B,G  (2x)

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

Reference :   A. Satoh, J. K. Kim, I. Miyahara, B. Devreese, I. Vandenberghe, A. Hacisalihoglu, T. Okajima, S. Kuroda, O. Adachi, J. A. Duine, J. Van Beeumen, K. Tanizawa, K. Hirotsu
Crystal Structure Of Quinohemoprotein Amine Dehydrogenase From Pseudomonas Putida. Identification Of A Novel Quinone Cofactor Encaged By Multiple Thioether Cross-Bridges.
J. Biol. Chem. V. 277 2830 2002
PubMed-ID: 11704672 | Reference-DOI: 10.1074/JBC.M109090200
(for further references see the PDB file header)

Molecule 1 - AMINE DEHYDROGENASE
	Chains	:	A
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	303

Molecule 2 - AMINE DEHYDROGENASE
	Chains	:	B
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	303

Molecule 3 - AMINE DEHYDROGENASE
	Chains	:	G
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	303

		1	2	3
Asymmetric Unit	:	A	B	G
Biological Unit 1 (1x)	:	A	B	G
Biological Unit 2 (2x)	:	A	B	G

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

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

Biological Unit 1 (2, 3)

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

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	HEC	4	Ligand/Ion	HEME C
2	NI	-1	Ligand/Ion	NICKEL (II) ION
3	TRQ	2	Mod. Amino Acid	2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1H-INDOL-3-YL)-PROPIONIC ACID

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:367 , HOH A:2068 , HOH A:2151 , HOH A:2248 , HIS B:11	BINDING SITE FOR RESIDUE NI A 2001
2	AC2	SOFTWARE	LYS A:32 , SER A:40 , ARG A:43 , THR A:99 , CYS A:100 , CYS A:103 , HIS A:104 , ARG A:108 , VAL A:109 , GLN A:112 , LEU A:122 , HIS A:126 , TRP A:130 , GLN A:136 , ASN A:489 , PRO A:491 , HEC A:1002 , HOH A:2058 , HOH A:2102 , HOH G:80 , HOH G:82	BINDING SITE FOR RESIDUE HEC A 1001
3	AC3	SOFTWARE	LYS A:11 , CYS A:12 , CYS A:15 , HIS A:16 , ARG A:26 , ILE A:27 , GLN A:30 , ARG A:43 , MET A:44 , HIS A:48 , LEU A:50 , ARG A:114 , PHE A:125 , HEC A:1001 , HOH A:2003 , HOH A:2035 , LEU B:116 , ASN B:117 , ASP B:118 , HIS B:119	BINDING SITE FOR RESIDUE HEC A 1002

Asymmetric Unit

No.	Residues
1	B:37	-	B:75

Asymmetric Unit

No.	Residues
1	Gln A:290	-	Pro A:291
2	Val A:371	-	Pro A:372
3	Gly B:44	-	Pro B:45
4	Asp G:12	-	Pro G:13
5	Gln G:28	-	Pro G:29

Asymmetric Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_QADG_PSEPU_001 *	S	62	T	QADG_PSEPU	---	---	G	S	62	T
2	UniProt	VAR_QADG_PSEPU_002 *	E	66	D	QADG_PSEPU	---	---	G	E	66	D
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_QADG_PSEPU_001 *	S	62	T	QADG_PSEPU	---	---	G	S	62	T
2	UniProt	VAR_QADG_PSEPU_002 *	E	66	D	QADG_PSEPU	---	---	G	E	66	D
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_QADG_PSEPU_001 *	S	62	T	QADG_PSEPU	---	---	G	S	62	T
2	UniProt	VAR_QADG_PSEPU_002 *	E	66	D	QADG_PSEPU	---	---	G	E	66	D
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 1JMX)

(no "Exon" information available for 1JMX)

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:493
 aligned with Q8VW85_PSEPU | Q8VW85 from UniProtKB/TrEMBL  Length:542

    Alignment length:493
                                    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       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539   
         Q8VW85_PSEPU    50 EQGPSLLQNKCMGCHIPEGNDTYSRISHQRKTPEGWLMSIARMQVMHGLQISDDDRRTLVKYLADKQGLAPSETDGVRYAMERRLNTVEQFDTQLSETCGRCHSGARVALQRRPAKEWEHLVNFHLGQWPSLEYQAQARDRDWLPIALQQVVPDLAKRYPLESAAWAEWQKARPKADALPGQWAFSGHMLAKGDVRGVMSVTPDQGDTFKVEVKGAYADGTPFNGSGSAILYNGYEWRGNVKVGDANLRQVFAALDGEMKGRMFEAEHDERGLDFTAVKEGKARLLAVQPAFIKAGGESEITLVGSGLAGKPDLGAGVEVTEVLEQTPTLVRLKARAAADAKPGQREVAVGTLKGVNLAVYDKVEEVKVVPAFSIARIGENGASVPKVQGRFEAEAWGKDANGQPLRIGYLPASWKVEPFNERAVEDEDVKFAGKMQADGVFVPGGAGPNPERKMMTNNAGNLKVIATLADGGQTGEGHMIVTVQRWNNPPLP 542
               SCOP domains d1jmxa1 A:2-85 Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2        d1jmxa2 A:86-162                                                             d1jmxa5 A:163-281 Quinohemoprotein amine dehydrogenase A chain, domain 3                                               d1jmxa3 A:282-363 Quinohemoprotein amine dehydrogenase A chain, domains 4 and 5   d1jmxa4 A:364-494 Quinohemoprotein amine dehydrogenase A chain, domains 4 and 5                                                     SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------1jmxA02 A:175-283 Quinohemoprotein amine dehydrogenase                                                       1jmxA03 A:284-362 Immunoglobulins                                              1jmxA04 A:363-486 Immunoglobulins                                                                                           -------- CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------Dehyd-heme_bind-1jmxA01 A:97-164                                    ----------------------------------------------------------------------------------------------------------------------DUF1927-1jmxA02 A:283-363                                                        ----DUF1928-1jmxA03 A:368-493                                                                                                     - Pfam domains
         Sec.struct. author .hhhhhhhhhhh....eee..ee.hhhhheehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhh.................hhhhhhhhh....hhhhhhee.hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhh.eeeeeeeee...eeeeeeeeeee....eeeeeeeeee....eeeeeeeeeee...eeeeeeee..eeeeeeeeee..eeeeeeee..eeeeeeeeeeee....eeeeee..eee...eeeeeeeee.....ee....eeeeeeeee...eeeeeeee......eeeeeee..eeeeeeeee....eeeee..eeeee............ee.eeeeeee.....eeeeee..eeeeeee.hhhhhhhhhhhhheee....eeee........hhhhh...eeeeeeeee.....eeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jmx A   2 EQGPSLLQNKCMGCHIPEGNDTYSRISHQRKTPEGWLMSIARMQVMHGLQISDDDRRTLVKYLADKQGLAPSETDGVRYAMERRLNTVEQFDTQLSETCGRCHSGARVALQRRPAKEWEHLVNFHLGQWPSLEYQAQARDRDWLPIALQQVVPDLAKRYPLESAAWAEWQKARPKADALPGQWAFSGHMLAKGDVRGVMSVTPDQGDTFKVEVKGAYADGTPFNGSGSAILYNGYEWRGNVKVGDANLRQVFAALDGEMKGRMFEAEHDERGLDFTAVKEGKARLLAVQPAFIKAGGESEITLVGSGLAGKPDLGAGVEVTEVLEQTPTLVRLKARAAADAKPGQREVAVGTLKGVNLAVYDKVEEVKVVPAFSIARIGENGASVPKVQGRFEAEAWGKDANGQPLRIGYLPASWKVEPFNERAVEDEDVKFAGKMQADGVFVPGGAGPNPERKMMTNNAGNLKVIATLADGGQTGEGHMIVTVQRWNNPPLP 494
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491

Chain B from PDB  Type:PROTEIN  Length:339
 aligned with Q8VW82_PSEPU | Q8VW82 from UniProtKB/TrEMBL  Length:379

    Alignment length:346
                                    43        53        63        73        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      
         Q8VW82_PSEPU    34 GPALKAGHEYMIVTNYPNNLHVVDVASDTVYKSCVMPDKFGPGTAMMAPDNRTAYVLNNHYGDIYGIDLDTCKNTFHANLSSVPGEVGRSMYSFAISPDGKEVYATVNPTQRLNDHYVVKPPRLEVFSTADGLEAKPVRTFPMPRQVYLMRAADDGSLYVAGPDIYKMDVKTGKYTVALPLRNWNRKGYSAPDVLYFWPHQSPRHEFSMLYTIARFKDDKQDPATADLLYGYLSVDLKTGKTHTQEFADLTELYFTGLRSPKDPNQIYGVLNRLAKYDLKQRKLIKAANLDHTYYCVAFDKKGDKLYLGGTFNDLAVFNPDTLEKVKNIKLPGGDMSTTTPQVFIR 379
               SCOP domains d1jmxb_ B: Quinohemoprotein amine dehydrogenase B chain                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1jmxB00 B:4-349 YVTN repeat-like/Quinoprotein amine dehydrogenase                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeee...eeeeee....eeeeeee........eeee.....eeeeee....eeeeee.....eeeeee......eeee....eee.....eeeeeeeeeee....eee...eeeeee.hhhhh....eeee.......eee.....eeee...eeee......eeeee..........................eeeeeeeeee.-------...eeeeeeeeee.....eeeeeeee....eeeeee......eeeeee.eeeeee....eeeeeee......eeee......eeee....eeeeee....eeeeeee...........eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jmx B   4 GPALKAGHEYMIVTNYPNNLHVVDVASDTVYKSCVMPDKFGPGTAMMAPDNRTAYVLNNHYGDIYGIDLDTCKNTFHANLSSVPGEVGRSMYSFAISPDGKEVYATVNPTQRLNDHYVVKPPRLEVFSTADGLEAKPVRTFPMPRQVYLMRAADDGSLYVAGPDIYKMDVKTGKYTVALPLRNWNRKGYSAPDVLYFWPHQSPRHEFSMLYTIARF-------ATADLLYGYLSVDLKTGKTHTQEFADLTELYFTGLRSPKDPNQIYGVLNRLAKYDLKQRKLIKAANLDHTYYCVAFDKKGDKLYLGGTFNDLAVFNPDTLEKVKNIKLPGGDMSTTTPQVFIR 349
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213     |   -   |   233       243       253       263       273       283       293       303       313       323       333       343      
                                                                                                                                                                                                                                                 219     227

Chain G from PDB  Type:PROTEIN  Length:77
 aligned with QADG_PSEPU | P0A182 from UniProtKB/Swiss-Prot  Length:79

    Alignment length:77
                                    12        22        32        42        52        62        72       
           QADG_PSEPU     3 AVAGCTATTDPGWEVDAFGGVSSLCQPMEADLYGCSDPCWWPAQVPDMMSTYQDWNAQASNSAEDWRNLGTVFPKDK  79
               SCOP domains d1jmxg_ G: Quinohemoprotein amine dehydrogenase C chain                       SCOP domains
               CATH domains 1jmxG00 G:3-79 Quinohemoprotein amine dehydrogenase                           CATH domains
               Pfam domains QH-AmDH_gamma-1jmxG01 G:3-79                                                  Pfam domains
         Sec.struct. author ..........................hhhhhhhhhhh.......................hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------T---D------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 1jmx G   3 AVAGCTATTDPGWEVDAFGGVSSLCQPMEADLYGCSDPCWwPAQVPDMMSTYQDWNAQASNSAEDWRNLGTVFPKDK  79
                                    12        22        32        42|       52        62        72       
                                                                   43-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 (Q8VW85_PSEPU | Q8VW85)


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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.

Chain B (Q8VW82_PSEPU | Q8VW82)

Chain G (QADG_PSEPU | P0A182)

molecular function
	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: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 Unit
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	Cis Peptide Bonds
		Asp G:12 - Pro G:13	[ RasMol ]
		Gln A:290 - Pro A:291	[ RasMol ]
		Gln G:28 - Pro G:29	[ RasMol ]
		Gly B:44 - Pro B:45	[ RasMol ]
		Val A:371 - Pro A:372	[ RasMol ]

Biological Units
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		Biological Unit 2	[ Jena3D ]

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	1jmx
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	Q8VW85_PSEPU \| Q8VW85
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	QADG_PSEPU \| P0A182	:	1jmz
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	Q8VW85_PSEPU \| Q8VW85	:	1jmz

1jmz	1JMZ CONTAINS THE SAME PROTEIN COMPLEXED WITH INHIBITOR

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (3, 3)

SS Bonds (1, 1)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (5, 7)

CATH Domains (4, 5)

Pfam Domains (4, 4)

Gene Ontology (7, 7)

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Entries Sharing at Least One Protein Chain (UniProt ID)

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