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Title :   MOLECULAR CLONING AND STRUCTURAL ANALYSIS OF QUINOHEMOPROTEIN ALCOHOL DEHYDROGENASE ADHIIG FROM PSEUDOMONAS PUTIDA HK5. COMPARIISON TO THE OTHER QUINOHEMOPROTEIN ALCOHOL DEHYDROGENASE ADHIIB FOUND IN THE SAME MICROORGANISM.

Authors :   H. Toyama, Z. W. Chen, M. Fukumoto, O. Adachi, K. Matsushita, F. S. Mathews

Date :   12 Jan 05 (Deposition) - 16 Aug 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A

Keywords :   Quinohemoprotein Alcohol Dehydrogenase, Electron Transfer, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Toyama, Z. W. Chen, M. Fukumoto, O. Adachi, K. Matsushita, F. S. Mathews
Molecular Cloning And Structural Analysis Of Quinohemoprotein Alcohol Dehydrogenase Adh-Iig From Pseudomonas Putida Hk5
J. Mol. Biol. V. 352 91 2005
PubMed-ID: 16061256 | Reference-DOI: 10.1016/J.JMB.2005.06.078
(for further references see the PDB file header)

Molecule 1 - QUINOHEMOPROTEIN ALCOHOL DEHYDROGENASE
	Chains	:	A
	EC Number	:	1.1.99.-
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	303
	Strain	:	HK5

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 6)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	PGR	3	Ligand/Ion	R-1,2-PROPANEDIOL
4	PQQ	1	Ligand/Ion	PYRROLOQUINOLINE QUINONE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:178 , ASN A:255 , ASP A:300 , PQQ A:801 , PGR A:803	BINDING SITE FOR RESIDUE CA A 802
2	AC2	SOFTWARE	GLU A:63 , CYS A:109 , CYS A:110 , VAL A:113 , ARG A:115 , THR A:160 , GLY A:175 , GLY A:176 , ALA A:177 , GLU A:178 , THR A:235 , TRP A:237 , ASN A:255 , ASP A:300 , LYS A:327 , TRP A:386 , ASP A:390 , TRP A:391 , PHE A:477 , ALA A:542 , CA A:802 , PGR A:803 , HOH A:1079 , HOH A:1108	BINDING SITE FOR RESIDUE PQQ A 801
3	AC3	SOFTWARE	ARG A:60 , GLY A:106 , TYR A:605 , CYS A:606 , GLN A:608 , CYS A:609 , HIS A:610 , LEU A:623 , LEU A:626 , LYS A:630 , LEU A:638 , ARG A:642 , ASP A:645 , GLY A:646 , MET A:647 , PHE A:650 , PHE A:654 , HOH A:1088 , HOH A:1303 , HOH A:1373	BINDING SITE FOR RESIDUE HEM A 901
4	AC4	SOFTWARE	CYS A:110 , GLU A:178 , ASP A:300 , TRP A:386 , ALA A:542 , PQQ A:801 , CA A:802 , HOH A:1271	BINDING SITE FOR RESIDUE PGR A 803
5	AC5	SOFTWARE	GLU A:441 , ILE A:595 , TYR A:665 , LYS A:668	BINDING SITE FOR RESIDUE PGR A 804
6	AC6	SOFTWARE	LEU A:552 , ARG A:579 , SER A:616 , ASP A:622 , ARG A:624 , LYS A:625 , HOH A:1201	BINDING SITE FOR RESIDUE PGR A 805

Asymmetric/Biological Unit

No.	Residues
1	A:109	-	A:110

Asymmetric/Biological Unit

No.	Residues
1	Ser A:257	-	Leu A:258
2	Leu A:272	-	Phe A:273
3	Thr A:382	-	Pro A:383

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	QGDA_PSEPU	622-699	1	A:593-670

(no "Exon" information available for 1YIQ)

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:684
 aligned with QGDA_PSEPU | Q4W6G0 from UniProtKB/Swiss-Prot  Length:718

    Alignment length:684
                                    39        49        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       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709    
           QGDA_PSEPU    30 ADIPANVDGARIIAADKEPGNWMSTGRTYDEQRYSPLKQISDQNVGQLGLAWSYKLDLDRGVEATPIVVDGAMYTTGPFSVVYALDARDGRLIWKYDPQSDRHRAGEACCDAVNRGVAVWKGKVYVGVLDGRLEAIDAKTGQRAWSVDTRADHKRSYTITGAPRVVNGKVVIGNGGAEFGVRGYVTAYDAETGKEAWRFYTVPGDPKLPPEGKGMEIAAKTWFGDAYVEQGGGGTAWDSFAYDPELNLLYIGVGNGSLWDPKWRSQAKGDNLFLSSIVAVNADTGEYVWHYQTTPGDAWDYTATQHMILAELPIDGKPRKVLMQAPKNGFFYVIDRATGELLSAKGIVPQSWTKGMDMKTGRPILDEENAAYWKNGKRNLVTPAFWGAHDWQPMSYNPDTGLVYIPAHIMSAYYEHIPEAPKRNPFKSMYQLGLRTGMMPEGAEGLLEMAKSWSGKLIAWDPVKQQAAWEVPYVTIFNGGTLSTAGNLVFEGSADGRVIAYAADTGEKLWEQPAASGVMAAPVTYSVDGEQYVTFMAGWGGAFSTFAGALSLRAGVQPYAQVLTYKLGGTAKLQEPAPRPDTPKPPALSNDTASIEAGAKLYDGYCSQCHGIHAVSGGVLPDLRKLTPEKHQMFLGILFGGRVPDGMPSFADAFTPEQVDQIHQYLIKRAHDLHQEGDTWKQFS 713
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 1yiqA01 A:1-578  [code=2.140.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhh...............ee........hhh.eeeeeeee...........eee..eeeee.hhh.eeeee.....eeeee....hhhhhhhh.........eee..eeeee....eeeeee.....eeeeee...............eee..eeee...........eeeeee.....eeeeee...........hhhhhhhhh.....hhhhhhee......eeee....eeeee...ee..hhhhhhh.........eeeeee.....eeeeee..............eeeeeeee..eeeeeeee.....eeeeee.....eeeeee......eeeee....eeeehhhhhh.......eee.............ee......eeeeeee..eeee...................ee.....hhhhhhhhhh..eeeeeeee....eeeeeeee.......eeee...eeeee....eeeeee.....eeeeee.........eeeee..eeeeeeee....hhhhhhhhhhhhhh.....eeeeeee.......................hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh..hhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTC  PDB: A:593-670 UniProt: 622-699                                         -------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1yiq A   1 ADIPANVDGARIIAADKEPGNWMSTGRTYDEQRYSPLKQISDQNVGQLGLAWSYKLDLDRGVEATPIVVDGVMYTTGPFSVVYALDARDGRLIWKYDPQSDRHRAGEACCDAVNRGVAVWKGKVYVGVLDGRLEAIDAKTGQRAWSVDTRADHKRSYTITGAPRVVNGKVVIGNGGAEFGVRGYVTAYDAETGKEAWRFYTVPGDPKLPPEGKGMEIAAKTWFGDAYVEQGGGGTAWDSFAYDPELNLLYIGVGNGSLWDPKWRSQAKGDNLFLSSIVAVNADTGEYVWHYQTTPGDAWDYTATQHMILAELPIDGKPRKVLMQAPKNGFFYVIDRATGELLSAKGIVPQSWTKGMDMKTGRPILDEENAAYWKNGKRNLVTPAFWGAHDWQPMSYNPDTGLVYIPAHIMSAYYEHIPEAPKRNPFKSMYQLGLRTGMMPEGAEGLLEMAKSWSGKLIAWDPVKQQAAWEVPYVTIFNGGTLSTAGNLVFEGSADGRVIAYAADTGEKLWEQPAASGVMAAPVTYSVDGEQYVTFMAGWGGAFSTFAGALSLRAGVQPYAQVLTYKLGGTAKLQEPAPRPDTPKPPALSNDTASIEAGAKLYDGYCSQCHGIHAVSGGVLPDLRKLTPEKHQMFLGILFGGRVPDGMPSFADAFTPEQVDQIHQYLIKRAHDLHQEGDTWKQFS 684
                                    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       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680

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 "SCOP Domain" information available for 1YIQ)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: 8 Propellor (110)

Topology: Methanol Dehydrogenase; Chain A (110)

Homologous Superfamily: [code=2.140.10.10, no name defined] (14)

Pseudomonas putida. Organism_taxid: 303. Strain: hk5 (1)

1yiqA01

A:1-578

(no "Pfam Domain" information available for 1YIQ)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (QGDA_PSEPU | Q4W6G0)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	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.
	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:0016614	oxidoreductase activity, acting on CH-OH group of donors	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
	GO:0070968	pyrroloquinoline quinone binding	Interacting selectively and non-covalently with pyrroloquinoline quinone, PQQ, the coenzyme or the prosthetic group of certain alcohol dehydrogenases and glucose dehydrogenases.
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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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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	Cis Peptide Bonds
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		Ser A:257 - Leu A:258	[ RasMol ]
		Thr A:382 - Pro A:383	[ RasMol ]

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1kv9	STRUCTURE AT 1.9 A RESOLUTION OF A QUINOHEMOPROTEIN ALCOHOL DEHYDROGENASE FROM PSEUDOMONAS PUTIDA HK5

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)

SS Bonds (1, 1)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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Gene Ontology (10, 10)

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