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Asym./Biol. Unit (Jmol Viewer)

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Title :   STRUCTURE REFINEMENT OF THE ALDEHYDE OXIDOREDUCTASE FROM DESULFOVIBRIO GIGAS AT 1.28 A

Authors :   J. M. Rebelo, J. M. Dias, R. Huber, J. J. G. Moura, M. J. Romao

Date :   20 Jul 04 (Deposition) - 27 Jul 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.28

Chains :   Asym./Biol. Unit : A

Keywords :   Aldehyde Oxidoreductase; Desulfovibrio Gigas; Iron-Sulphur Cluster (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. M. Rebelo, J. M. Dias, R. Huber, J. J. G. Moura, M. J. Romao
Structure Refinement Of The Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop) At 1. 28 A
J. Biol. Inorg. Chem. V. 6 791 2001
PubMed-ID: 11713686 | Reference-DOI: 10.1007/S007750100255
(for further references see the PDB file header)

Molecule 1 - ALDEHYDE OXIDOREDUCTASE
	Chains	:	A
	EC Number	:	1.2.3.1
	Organism Scientific	:	DESULFOVIBRIO GIGAS
	Organism Taxid	:	879
	Synonym	:	MOLYBDENUM IRON SULFUR PROTEIN

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 10)

No.	Name	Count	Type	Full Name
1	CL	3	Ligand/Ion	CHLORIDE ION
2	FES	2	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
3	IPA	2	Ligand/Ion	ISOPROPYL ALCOHOL
4	MG	2	Ligand/Ion	MAGNESIUM ION
5	PCD	1	Ligand/Ion	(MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:460 , TYR A:535 , GLN A:539	BINDING SITE FOR RESIDUE CL A 916
02	AC2	SOFTWARE	ASP A:263 , GLU A:899 , GLU A:903 , HOH A:4178 , HOH A:4272 , HOH A:4345	BINDING SITE FOR RESIDUE MG A 917
03	AC3	SOFTWARE	TYR A:892 , ARG A:893 , HOH A:4194 , HOH A:5012	BINDING SITE FOR RESIDUE CL A 918
04	AC4	SOFTWARE	HOH A:4217 , HOH A:4424 , HOH A:4801 , HOH A:4802 , HOH A:4950 , HOH A:5038	BINDING SITE FOR RESIDUE MG A 919
05	AC5	SOFTWARE	LYS A:248 , PRO A:898 , GLU A:899 , HOH A:4410 , HOH A:4546	BINDING SITE FOR RESIDUE CL A 920
06	AC6	SOFTWARE	GLN A:99 , CYS A:139 , THR A:420 , PHE A:421 , GLY A:422 , ALA A:531 , PHE A:532 , ARG A:533 , TRP A:650 , HIS A:653 , GLY A:654 , GLN A:655 , GLY A:656 , GLY A:660 , SER A:695 , GLY A:696 , GLY A:697 , SER A:698 , ARG A:699 , GLN A:700 , GLN A:701 , LEU A:795 , SER A:797 , CYS A:799 , ASN A:800 , THR A:804 , GLN A:807 , ALA A:864 , SER A:865 , GLY A:866 , VAL A:867 , GLY A:868 , GLU A:869 , IPA A:914 , HOH A:4127 , HOH A:4395	BINDING SITE FOR RESIDUE PCD A 921
07	AC7	SOFTWARE	GLN A:99 , CYS A:100 , GLY A:101 , CYS A:103 , CYS A:137 , ARG A:138 , CYS A:139 , ILE A:368	BINDING SITE FOR RESIDUE FES A 908
08	AC8	SOFTWARE	GLY A:39 , CYS A:40 , GLU A:41 , GLY A:43 , GLN A:44 , CYS A:45 , GLY A:46 , CYS A:48 , ARG A:58 , CYS A:60	BINDING SITE FOR RESIDUE FES A 909
09	AC9	SOFTWARE	ALA A:531 , TYR A:535 , GLY A:697 , PCD A:921 , HOH A:4375	BINDING SITE FOR RESIDUE IPA A 914
10	BC1	SOFTWARE	VAL A:5 , GLU A:12 , ASN A:14 , PRO A:416 , TRP A:683 , HOH A:4047	BINDING SITE FOR RESIDUE IPA A 915

(no "SS Bond" information available for 1VLB)

Asymmetric/Biological Unit

No.	Residues
1	Leu A:894	-	Pro A:895

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	2FE2S_FER_2	PS51085	2Fe-2S ferredoxin-type iron-sulfur binding domain profile.	MOP_DESGI	2-79	1	A:2-79
2	2FE2S_FER_1	PS00197	2Fe-2S ferredoxin-type iron-sulfur binding region signature.	MOP_DESGI	40-48	1	A:40-48

(no "Exon" information available for 1VLB)

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:907
 aligned with MOP_DESGI | Q46509 from UniProtKB/Swiss-Prot  Length:907

    Alignment length:907
                                    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       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       
            MOP_DESGI     1 MIQKVITVNGIEQNLFVDAEALLSDVLRQQLGLTGVKVGCEQGQCGACSVILDGKVVRACVTKMKRVADGAQITTIEGVGQPENLHPLQKAWVLHGGAQCGFCSPGFIVSAKGLLDTNADPSREDVRDWFQKHRNACRCTGYKPLVDAVMDAAAVINGKKPETDLEFKMPADGRIWGSKYPRPTAVAKVTGTLDYGADLGLKMPAGTLHLAMVQAKVSHANIKGIDTSEALTMPGVHSVITHKDVKGKNRITGLITFPTNKGDGWDRPILCDEKVFQYGDCIALVCADSEANARAAAEKVKVDLEELPAYMSGPAAAAEDAIEIHPGTPNVYFEQPIVKGEDTGPIFASADVTVEGDFYVGRQPHMPIEPDVAFAYMGDDGKCYIHSKSIGVHLHLYMIAPGVGLEPDQLVLVANPMGGTFGYKFSPTSEALVAVAAMATGRPVHLRYNYQQQQQYTGKRSPWEMNVKFAAKKDGTLLAMESDWLVDHGPYSEFGDLLTLRGAQFIGAGYNIPNIRGLGRTVATNHVWGSAFRGYGAPQSMFASECLMDMLAEKLGMDPLELRYKNAYRPGDTNPTGQEPEVFSLPDMIDQLRPKYQAALEKAQKESTATHKKGVGISIGVYGSGLDGPDASEAWAELNADGTITVHTAWEDHGQGADIGCVGTAHEALRPMGVAPEKIKFTWPNTATTPNSGPSGGSRQQVMTGNAIRVACENLLKACEKPGGGYYTYDELKAADKPTKITGNWTASGATHCDAVTGLGKPFVVYMYGVFMAEVTVDVATGQTTVDGMTLMADLGSLCNQLATDGQIYGGLAQGIGLALSEDFEDIKKHATLVGAGFPFIKQIPDKLDIVYVNHPRPDGPFGASGVGELPLTSPHAAIINAIKSATGVRIYRLPAYPEKVLEALKA 907
               SCOP domains d1vlba2 A:1-80 Aldehyde oxidoreductase, N-terminal domain                       d1vlba1 A:81-193 Aldehyde oxidoreductase, domain 2                                                               d1vlba3 A:194-310 Aldehyde oxidoreductase, domain 3                                                                  d1vlba4 A:311-907 Aldehyde oxidoreductase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1vlbA01 A:1-74  [code=3.10.20.30, no name defined]                        1vlbA02 A:75-193  [code=1.10.150.120, no name defined]                                                                 --------------1vlbA03 A:208-308  [code=3.90.1170.50, no name defined]                                              ----------------------1vlbA04 A:331-364,A:458-580       1vlbA05 A:365-457 Aldehyde Oxidoreductase; domain 4                                          1vlbA04 A:331-364,A:458-580 Aldehyde Oxidoreductase; domain 4                                                              1vlbA07 A:581-624,A:751-907                 1vlbA06 A:625-750 Aldehyde Oxidoreductase; domain 4                                                                           1vlbA07 A:581-624,A:751-907 Aldehyde Oxidoreductase; domain 4                                                                                                 CATH domains
               Pfam domains -----Fer2-1vlbA01 A:6-73                                                 -Fer2_2-1vlbA02 A:75-151                                                      --------------------------------------Ald_Xan_dh_C-1vlbA04 A:190-308                                                                                         ------Ald_Xan_dh_C2-1vlbA03 A:315-845                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    -------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeeee....hhhhhhhhh..................eeee..eeee.hhh.hhhh....eeehhhhhh.....hhhhhhhhhhh......hhhhhhhhhhhhhh.....hhhhhhhhhhhh........hhhhhhhhhhhhhhhh...hhhhhh.................hhhhhhh....hhhhhhhh.....eeeeeee.....eeeeeeehhhhhh...eeeeehhhhh....ee...............ee.....ee.....eeeeeee.hhhhhhhhhh..eeeeee.....hhhhhhh............eeeeeeeee..hhhhhhhhh.eeeeeeeee...........eeeeee.....eeeee...hhhhhhhhhhhhhh.hhh.eeeee.......hhhhh..hhhhhhhhhhhhh..eeee.hhhhhhhh......eeeeeeeee.....eeeeeeeeeee......hhhhhhhhhhhhh.......eeeeeeeee.............hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeeeee.......eeeeeeee.....eeee........hhhhhhhhhhhhhhhhhh.hhh.eee.................hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh....eeeeeee...................eeeeeeeeeeeee.....eeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..................hhhhh...eeeee.......hhhhh....hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -2FE2S_FER_2  PDB: A:2-79 UniProt: 2-79                                        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) ---------------------------------------2FE2S_FER------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vlb A   1 MIQKVITVNGIEQNLFVDAEALLSDVLRQQLGLTGVKVGCEQGQCGACSVILDGKVVRACVTKMKRVADGAQITTIEGVGQPENLHPLQKAWVLHGGAQCGFCSPGFIVSAKGLLDTNADPSREDVRDWFQKHRNACRCTGYKPLVDAVMDAAAVINGKKPETDLEFKMPADGRIWGSKYPRPTAVAKVTGTLDYGADLGLKMPAGTLHLAMVQAKVSHANIKGIDTSEALTMPGVHSVITHKDVKGKNRITGLITFPTNKGDGWDRPILCDEKVFQYGDCIALVCADSEANARAAAEKVKVDLEELPAYMSGPAAAAEDAIEIHPGTPNVYFEQPIVKGEDTGPIFASADVTVEGDFYVGRQPHMPIEPDVAFAYMGDDGKCYIHSKSIGVHLHLYMIAPGVGLEPDQLVLVANPMGGTFGYKFSPTSEALVAVAAMATGRPVHLRYNYQQQQQYTGKRSPWEMNVKFAAKKDGTLLAMESDWLVDHGPYSEFGDLLTLRGAQFIGAGYNIPNIRGLGRTVATNHVWGSAFRGYGAPQSMFASECLMDMLAEKLGMDPLELRYKNAYRPGDTNPTGQEPEVFSLPDMIDQLRPKYQAALEKAQKESTATHKKGVGISIGVYGSGLDGPDASEAWAELNADGTITVHTAWEDHGQGADIGCVGTAHEALRPMGVAPEKIKFTWPNTATTPNSGPSGGSRQQVMTGNAIRVACENLLKACEKPGGGYYTYDELKAADKPTKITGNWTASGATHCDAVTGLGKPFVVYMYGVFMAEVTVDVATGQTTVDGMTLMADLGSLCNQLATDGQIYGGLAQGIGLALSEDFEDIKKHATLVGAGFPFIKQIPDKLDIVYVNHPRPDGPFGASGVGELPLTSPHAAIINAIKSATGVRIYRLPAYPEKVLEALKA 907
                                    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       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900

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

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Fer2 (69)

Family: Fer2 (60)

Desulfovibrio gigas (2)

Fer2-1vlbA01

A:6-73

Family: Fer2_2 (24)

Desulfovibrio gigas (2)

Fer2_2-1vlbA02

A:75-151

Clan: no clan defined [family: Ald_Xan_dh_C2] (24)

Family: Ald_Xan_dh_C2 (24)

Desulfovibrio gigas (2)

Ald_Xan_dh_C2-1vlbA03

A:315-845

Clan: no clan defined [family: Ald_Xan_dh_C] (24)

Family: Ald_Xan_dh_C (24)

Desulfovibrio gigas (2)

Ald_Xan_dh_C-1vlbA04

A:190-308

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (MOP_DESGI | Q46509)

molecular function
	GO:0051537	2 iron, 2 sulfur cluster binding	Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
	GO:0033727	aldehyde dehydrogenase (FAD-independent) activity	Catalysis of the reaction: an aldehyde + H2O + acceptor = a carboxylate + reduced acceptor.
	GO:0009055	electron transfer 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:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	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.
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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Leu A:894 - Pro A:895	[ RasMol ]

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	1vlb
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	MOP_DESGI \| Q46509	:	1sij 3fah 3fc4 3l4p 4c7y 4c7z 4c80 4us8 4us9 4usa

1dgj	A CLOSELY RELATED ENZYME

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (4, 4)

CATH Domains (4, 7)

Pfam Domains (4, 4)

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