1KV9 - JenaLib

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Title :   STRUCTURE AT 1.9 A RESOLUTION OF A QUINOHEMOPROTEIN ALCOHOL DEHYDROGENASE FROM PSEUDOMONAS PUTIDA HK5

Authors :   Z. -W. Chen, K. Matsushita, T. Yamashita, T. Fujii, H. Toyama, O. Adachi H. D. Bellamy, F. S. Mathews

Date :   25 Jan 02 (Deposition) - 10 Jul 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

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

Reference :   Z. W. Chen, K. Matsushita, T. Yamashita, T. A. Fujii, H. Toyama, O. Adachi, H. D. Bellamy, F. S. Mathews
Structure At 1. 9 A Resolution Of A Quinohemoprotein Alcohol Dehydrogenase From Pseudomonas Putida Hk5.
Structure V. 10 837 2002
PubMed-ID: 12057198 | Reference-DOI: 10.1016/S0969-2126(02)00774-8
(for further references see the PDB file header)

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

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 6)

No.	Name	Count	Type	Full Name
1	ACN	1	Ligand/Ion	ACETONE
2	CA	1	Ligand/Ion	CALCIUM ION
3	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4	GOL	1	Ligand/Ion	GLYCEROL
5	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
6	PQQ	1	Ligand/Ion	PYRROLOQUINOLINE QUINONE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:173 , ASN A:250 , ASP A:295 , PQQ A:801	BINDING SITE FOR RESIDUE CA A 802
2	AC2	SOFTWARE	GLU A:59 , CYS A:105 , CYS A:106 , VAL A:109 , ARG A:111 , THR A:155 , GLY A:170 , GLY A:171 , ALA A:172 , GLU A:173 , THR A:230 , TRP A:232 , ASN A:250 , ASP A:295 , LYS A:322 , ASN A:382 , TRP A:383 , TRP A:460 , GLY A:524 , VAL A:525 , CA A:802 , ACN A:803 , HOH A:1114 , HOH A:1210	BINDING SITE FOR RESIDUE PQQ A 801
3	AC3	SOFTWARE	ALA A:101 , ARG A:102 , PHE A:590 , CYS A:591 , CYS A:594 , HIS A:595 , ILE A:605 , PRO A:606 , LEU A:608 , SER A:611 , PHE A:619 , VAL A:623 , LEU A:631 , MET A:633 , PHE A:636 , LEU A:640 , HOH A:1091 , HOH A:1139 , HOH A:1242 , HOH A:1362 , HOH A:1514	BINDING SITE FOR RESIDUE HEM A 901
4	AC4	SOFTWARE	TRP A:48 , ALA A:83 , ALA A:84 , SER A:85 , TYR A:515 , HOH A:1178 , HOH A:1528 , HOH A:1614 , HOH A:1683 , HOH A:1687 , HOH A:1735	BINDING SITE FOR RESIDUE EPE A 804
5	AC5	SOFTWARE	GLU A:173 , ASP A:295 , LYS A:322 , PRO A:377 , PQQ A:801	BINDING SITE FOR RESIDUE ACN A 803
6	AC6	SOFTWARE	ASP A:51 , LEU A:52 , SER A:543 , HOH A:1392 , HOH A:1531	BINDING SITE FOR RESIDUE GOL A 805

Asymmetric/Biological Unit

No.	Residues
1	A:105	-	A:106

Asymmetric/Biological Unit

No.	Residues
1	Ser A:252	-	Pro A:253
2	Leu A:267	-	Tyr A:268
3	Trp A:374	-	Pro A:375

(no "SAP(SNP)/Variant" information available for 1KV9)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BACTERIAL_PQQ_2	PS00364	Bacterial quinoprotein dehydrogenases signature 2.	QHED_PSEPU	254-275	1	A:232-253
2	CYTC	PS51007	Cytochrome c family profile.	QHED_PSEPU	600-678	1	A:578-656

(no "Exon" information available for 1KV9)

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:664
 aligned with QHED_PSEPU | Q8GR64 from UniProtKB/Swiss-Prot  Length:690

    Alignment length:664
                                    32        42        52        62        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       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682    
           QHED_PSEPU    23 AGVDEAAIRATEQAGGEWLSHGRTYAEQRFSPLKQIDASNVRSLGLAWYMDLDNTRGLEATPLFHDGVIYTSMSWSRVIAVDAASGKELWRYDPEVAKVKARTSCCDAVNRGVALWGDKVYVGTLDGRLIALDAKTGKAIWSQQTTDPAKPYSITGAPRVVKGKVIIGNGGAEYGVRGFVSAYDADTGKLAWRFYTVPGDPALPYEHPELREAAKTWQGDQYWKLGGGGTVWDSMAYDPELDLLYVGTGNGSPWNREVRSPGGGDNLYLSSILAIRPDTGKLAWHYQVTPGDSWDFTATQQITLAELNIDGKPRKVLMQAPKNGFFYVLDRTNGKLISAEKFGKVTWAEKVDLATGRPVEAPGVRYEKEPIVMWPSPFGAHNWHSMSFNPGTGLVYIPYQEVPGVYRNEGKDFVTRKAFNTAAGFADATDVPAAVVSGALLAWDPVKQKAAWKVPYPTHWNGGTLSTAGNLVFQGTAAGQMHAYSADKGEALWQFEAQSGIVAAPMTFELAGRQYVAIMAGWGGVATLTGGESMNLPGMKNRSRLLVFALDGKAQLPPPAPAPAKVERVPQPVTAAPEQVQAGKQLYGQFCSVCHGMGTISGGLIPDLRQSSDATREHFQQIVLQGALKPLGMPSFDDSLKPEEVEQIKLYVMSREYEDYMARH 686
               SCOP domains d1kv9a2 A:1-560 Quinoprotein alcohol dehydrogenase, N-terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           d1kv9a1 A:561-664 Quinoprotein alcohol dehydrogenase, C-terminal domain                                  SCOP domains
               CATH domains 1kv9A01 A:1-561  [code=2.140.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             1kv9A02 A:562-664 Cytochrome c                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh..................ee........hhh.eeeeeeee...........eee..eeeeeehhheeeeee.....eeeee....hhhhhhhh.........eee..eeeee....eeeeee.....eeeeee..............eee..eeee...........eeeeee.....eeeeee...........hhhhhhhhh.....hhhhhhee......eeee....eeeee...ee..hhhhhh..........eeeee......eeeeee..............eeeeeeee..eeeeeeee.....eeeeee.....eeeeee......eeee......eee..........eee.............eee....eeeeeeee..eee..hhhhh..........hhhhh...hhhhheeeeeeee....eeeeeeee.......eeee...eeeee....eeeeee.....eeeeee.........eeeee..eeeeeeee...hhhhhhhhhhhhh.......eeeeeee.........................hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.hhhhh........hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------BACTERIAL_PQQ_2       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTC  PDB: A:578-656 UniProt: 600-678                                          -------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kv9 A   1 AGVDEAAIRATEQAGGEWLSHGRTYAEQRFSPLKQIDASNVRSLGLAWYMDLDNTRGLEATPLFHDGVIYTSMSWSRVIAVDAASGKELWRYDPEVAKVKARTSCCDAVNRGVALWGDKVYVGTLDGRLIALDAKTGKAIWSQQTTDPAKPYSITGAPRVVKGKVIIGNGGAEYGVRGFVSAYDADTGKLAWRFYTVPGDPALPYEHPELREAAKTWQGDQYWKLGGGGTVWDSMAYDPELDLLYVGTGNGSPWNREVRSPGGGDNLYLSSILAIRPDTGKLAWHYQVTPGDSWDFTATQQITLAELNIDGKPRKVLMQAPKNGFFYVLDRTNGKLISAEKFGKVTWAEKVDLATGRPVEAPGVRYEKEPIVMWPSPFGAHNWHSMSFNPGTGLVYIPYQEVPGVYRNEGKDFVTRKAFNTAAGFADATDVPAAVVSGALLAWDPVKQKAAWKVPYPTHWNGGTLSTAGNLVFQGTAAGQMHAYSADKGEALWQFEAQSGIVAAPMTFELAGRQYVAIMAGWGGVATLTGGESMNLPGMKNRSRLLVFALDGKAQLPPPAPAPAKVERVPQPVTAAPEQVQAGKQLYGQFCSVCHGMGTISGGLIPDLRQSSDATREHFQQIVLQGALKPLGMPSFDDSLKPEEVEQIKLYVMSREYEDYMARH 664
                                    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

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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Cytochrome Bc1 Complex; Chain D, domain 2 (279)

Homologous Superfamily: Cytochrome c (279)

Pseudomonas putida. Organism_taxid: 303 (1)

1kv9A02

A:562-664

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 (1)

1kv9A01

A:1-561

(no "Pfam Domain" information available for 1KV9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (QHED_PSEPU | Q8GR64)

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: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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4aah	DETERMINATION OF THE GENE SEQUENCE AND THE THREE- DIMENSIONAL STRUCTURE AT 2.4 A RESOLUTION OF METHANOL DEHYDROGENASE FROM METHYLOPHILUS W3A1

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 6)

Sites (6, 6)

SS Bonds (1, 1)

Cis Peptide Bonds (3, 3)

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