Pyruvate-flavodoxin oxidoreductase - Desulfovibrio africanus

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P94692 (P94692_DESAF) Unreviewed, UniProtKB/TrEMBL

Last modified January 25, 2012. Version 80. History...

Clusters with 100%, 90%, 50% identity |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info Customize order

Names and origin

Protein names

Recommended name:
Pyruvate-flavodoxin oxidoreductase PIRNR PIRNR000159
EC=1.2.7.- PIRNR PIRNR000159

Gene names

Name:

por EMBL CAA70873.1

Organism

Desulfovibrio africanus EMBL CAA70873.1

Taxonomic identifier

873 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Deltaproteobacteria › Desulfovibrionales › Desulfovibrionaceae › Desulfovibrio

Protein attributes

Sequence length	1232 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin By similarity. PIRNR PIRNR000159
Catalytic activity	Pyruvate + CoA + oxidized flavodoxin = acetyl-CoA + CO₂ + reduced flavodoxin. PIRNR PIRNR000159
Sequence similarities	Belongs to the nifJ family. PIRNR PIRNR000159

Ontologies

Keywords
Biological process	Electron transport PIRNR PIRNR000159 Transport
Ligand	4Fe-4S RuleBase RU003429 PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 1KEK PDB 2UZA Calcium PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 1KEK PDB 2UZA Iron Iron-sulfur Magnesium PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 1KEK PDB 2UZA Metal-binding Pyruvate EMBL CAA70873.1 Thiamine pyrophosphate PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 1B0P
Molecular function	Oxidoreductase PIRNR PIRNR000159
Technical term	3D-structure PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 1KEK PDB 2UZA
Gene Ontology (GO)
Biological process	electron transport chain Inferred from electronic annotation. Source: UniProtKB-KW transport Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	4 iron, 4 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW electron carrier activity Inferred from electronic annotation. Source: InterPro iron ion binding Inferred from electronic annotation. Source: InterPro oxidoreductase activity, acting on the aldehyde or oxo group of donors Inferred from electronic annotation. Source: InterPro thiamine pyrophosphate binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Regions

Region

962 – 965

Thiamine pyrophosphate binding PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 1B0P

Region

991 – 996

Thiamine pyrophosphate binding PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 1B0P

Sites

Metal binding

689

Iron-sulfur (4Fe-4S) 3 PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 1KEK PDB 2UZA

Metal binding

690

Iron-sulfur (4Fe-4S) 3; via amide nitrogen PDB 2PDA

Metal binding

692

Iron-sulfur (4Fe-4S) 3 PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 1KEK PDB 2UZA

Metal binding

693

Iron-sulfur (4Fe-4S) 3; via amide nitrogen PDB 2C3M PDB 2C3O PDB 2C42 PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 2UZA

Metal binding

695

Iron-sulfur (4Fe-4S) 3 PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 1KEK PDB 2UZA

Metal binding

699

Iron-sulfur (4Fe-4S) 2 PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 1KEK PDB 2UZA

Metal binding

745

Iron-sulfur (4Fe-4S) 2 PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 1KEK PDB 2UZA

Metal binding

748

Iron-sulfur (4Fe-4S) 2 PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 1KEK PDB 2UZA

Metal binding

749

Iron-sulfur (4Fe-4S) 2; via amide nitrogen PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 1KEK PDB 2UZA

Metal binding

751

Iron-sulfur (4Fe-4S) 2 PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 1KEK PDB 2UZA

Metal binding

755

Iron-sulfur (4Fe-4S) 3 PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 1KEK PDB 2UZA

Metal binding

761

Iron-sulfur (4Fe-4S) 3 PDB 2PDA

Metal binding

812

Iron-sulfur (4Fe-4S) 1 PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 1KEK PDB 2UZA

Metal binding

815

Iron-sulfur (4Fe-4S) 1 PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 1KEK PDB 2UZA

Metal binding

840

Iron-sulfur (4Fe-4S) 1 PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 1KEK PDB 2UZA

Metal binding

963

Magnesium PDB 2C3M PDB 2C3O PDB 2C42 PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 1KEK PDB 2UZA

Metal binding

983

Calcium PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 1KEK PDB 2UZA

Metal binding

985

Calcium PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 1KEK PDB 2UZA

Metal binding

991

Magnesium PDB 2C3M PDB 2C3O PDB 2C42 PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 1KEK PDB 2UZA

Metal binding

993

Magnesium PDB 2C3M PDB 2C3O PDB 2C42 PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 1KEK PDB 2UZA

Metal binding

1056

Calcium; via carbonyl oxygen PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 1KEK PDB 2UZA

Metal binding

1057

Calcium; via carbonyl oxygen PDB 2C3O PDB 1B0P

Metal binding

1059

Calcium; via carbonyl oxygen PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 1KEK PDB 2UZA

Metal binding

1061

Calcium; via carbonyl oxygen PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 1KEK PDB 2UZA

Metal binding

1063

Calcium PDB 2C3M PDB 2C42 PDB 2PDA PDB 2C3P PDB 2C3Y

Metal binding

1071

Iron-sulfur (4Fe-4S) 1 PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 2C3P PDB 2C3U PDB 2C3Y PDB 1B0P PDB 1KEK PDB 2UZA

Binding site

Thiamine pyrophosphate PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 1B0P

Binding site

Thiamine pyrophosphate PDB 2C3M PDB 2C3O PDB 2C42 PDB 1B0P

Binding site

817

Thiamine pyrophosphate PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 1B0P

Binding site

840

Thiamine pyrophosphate PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 1B0P

Binding site

869

Thiamine pyrophosphate PDB 2C3M PDB 2C3O PDB 2C42 PDB 2PDA PDB 1B0P

Sequences

Sequence

Length

Mass (Da)

Tools

P94692 [UniParc].

Last modified May 1, 1997. Version 1.
Checksum: 55D84F536CCFFDBF
Show »

FASTA

1,232

133,680

        10         20         30         40         50         60 
MGKKMMTTDG NTATAHVAYA MSEVAAIYPI TPSSTMGEEA DDWAAQGRKN IFGQTLTIRE 

        70         80         90        100        110        120 
MQSEAGAAGA VHGALAAGAL TTTFTASQGL LLMIPNMYKI SGELLPGVFH VTARAIAAHA 

       130        140        150        160        170        180 
LSIFGDHQDI YAARQTGFAM LASSSVQEAH DMALVAHLAA IESNVPFMHF FDGFRTSHEI 

       190        200        210        220        230        240 
QKIEVLDYAD MASLVNQKAL AEFRAKSMNP EHPHVRGTAQ NPDIYFQGRE AANPYYLKVP 

       250        260        270        280        290        300 
GIVAEYMQKV ASLTGRSYKL FDYVGAPDAE RVIVSMGSSC ETIEEVINHL AAKGEKIGLI 

       310        320        330        340        350        360 
KVRLYRPFVS EAFFAALPAS AKVITVLDRT KEPGAPGDPL YLDVCSAFVE RGEAMPKILA 

       370        380        390        400        410        420 
GRYGLGSKEF SPAMVKSVYD NMSGAKKNHF TVGIEDDVTG TSLPVDNAFA DTTPKGTIQC 

       430        440        450        460        470        480 
QFWGLGADGT VGANKQAIKI IGDNTDLFAQ GYFSYDSKKS GGITISHLRF GEKPIQSTYL 

       490        500        510        520        530        540 
VNRADYVACH NPAYVGIYDI LEGIKDGGTF VLNSPWSSLE DMDKHLPSGI KRTIANKKLK 

       550        560        570        580        590        600 
FYNIDAVKIA TDVGLGGRIN MIMQTAFFKL AGVLPFEKAV DLLKKSIHKA YGKKGEKIVK 

       610        620        630        640        650        660 
MNTDAVDQAV TSLQEFKYPD SWKDAPAETK AEPMTNEFFK NVVKPILTQQ GDKLPVSAFE 

       670        680        690        700        710        720 
ADGRFPLGTS QFEKRGVAIN VPQWVPENCI QCNQCAFVCP HSAILPVLAK EEELVGAPAN 

       730        740        750        760        770        780 
FTALEAKGKE LKGYKFRIQI NTLDCMGCGN CADICPPKEK ALVMQPLDTQ RDAQVPNLEY 

       790        800        810        820        830        840 
AARIPVKSEV LPRDSLKGSQ FQEPLMEFSG ACSGCGETPY VRVITQLFGE RMFIANATGC 

       850        860        870        880        890        900 
SSIWGASAPS MPYKTNRLGQ GPAWGNSLFE DAAEYGFGMN MSMFARRTHL ADLAAKALES 

       910        920        930        940        950        960 
DASGDVKEAL QGWLAGKNDP IKSKEYGDKL KKLLAGQKDG LLGQIAAMSD LYTKKSVWIF 

       970        980        990       1000       1010       1020 
GGDGWAYDIG YGGLDHVLAS GEDVNVFVMD TEVYSNTGGQ SSKATPTGAV AKFAAAGKRT 

      1030       1040       1050       1060       1070       1080 
GKKDLARMVM TYGYVYVATV SMGYSKQQFL KVLKEAESFP GPSLVIAYAT CINQGLRKGM 

      1090       1100       1110       1120       1130       1140 
GKSQDVMNTA VKSGYWPLFR YDPRLAAQGK NPFQLDSKAP DGSVEEFLMA QNRFAVLDRS 

      1150       1160       1170       1180       1190       1200 
FPEDAKRLRA QVAHELDVRF KELEHMAATN IFESFAPAGG KADGSVDFGE GAEFCTRDDT 

      1210       1220       1230 
PMMARPDSGE ACDQNRAGTS EQQGDLSKRT KK

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References

[1]	"Isolation and analysis of the gene encoding the pyruvate-ferredoxin oxidoreductase of Desulfovibrio africanus, production of the recombinant enzyme in Escherichia coli, and effect of carboxy-terminal deletions on its stability." Pieulle L., Magro V., Hatchikian E.C. J. Bacteriol. 179:5684-5692(1997) [PubMed: 9294422] [Abstract] Cited for: NUCLEOTIDE SEQUENCE. Strain: NCIB 8401 EMBL CAA70873.1.
[2]	Claude H. Submitted (NOV-1996) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE. Strain: NCIB 8401 EMBL CAA70873.1.
[3]	"Crystal structures of the key anaerobic enzyme pyruvate:ferredoxin oxidoreductase, free and in complex with pyruvate." Chabriere E., Charon M.H., Volbeda A., Pieulle L., Hatchikian E.C., Fontecilla-Camps J.C. Nat. Struct. Biol. 6:182-190(1999) [PubMed: 10048931] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.31 ANGSTROMS) OF 2-1232 IN COMPLEX WITH CALCIUM; IRON-SULFUR (4FE-4S); MAGNESIUM AND THIAMINE PYROPHOSPHATE.
[4]	"Crystal structure of the free radical intermediate of pyruvate:ferredoxin oxidoreductase." Chabriere E., Vernede X., Guigliarelli B., Charon M.H., Hatchikian E.C., Fontecilla-Camps J.C. Science 294:2559-2563(2001) [PubMed: 11752578] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 2-1232 IN COMPLEX WITH CALCIUM; IRON-SULFUR (4FE-4S) AND MAGNESIUM.
[5]	"Flexibility of thiamine diphosphate revealed by kinetic crystallographic studies of the reaction of pyruvate-ferredoxin oxidoreductase with pyruvate." Cavazza C., Contreras-Martel C., Pieulle L., Chabriere E., Hatchikian E.C., Fontecilla-Camps J.C. Structure 14:217-224(2006) [PubMed: 16472741] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.78 ANGSTROMS) OF 2-1232 IN COMPLEX WITH CALCIUM; IRON-SULFUR (4FE-4S); MAGNESIUM AND THIAMINE PYROPHOSPHATE.
[6]	"Pyruvate:Ferredoxin Oxidoreductase." Chabriere E., Cavazza C., Contreras-Martel C., Fontecilla-Camps J.C. Submitted (APR-2007) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (2.42 ANGSTROMS) OF 2-1232 IN COMPLEX WITH CALCIUM; IRON-SULFUR (4FE-4S) AND MAGNESIUM.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Y09702 Genomic DNA. Translation: CAA70873.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1B0P	X-ray	2.31	A/B	2-1232	[»]
1KEK	X-ray	1.90	A/B	2-1232	[»]
2C3M	X-ray	1.84	A/B	2-1232	[»]
2C3O	X-ray	2.70	A/B	2-1232	[»]
2C3P	X-ray	2.33	A/B	2-1232	[»]
2C3U	X-ray	2.32	A/B	2-1232	[»]
2C3Y	X-ray	1.93	A/B	2-1232	[»]
2C42	X-ray	1.78	A/B	2-1232	[»]
2PDA	X-ray	3.00	A/B	2-1232	[»]
2UZA	X-ray	2.42	A/B	2-1232	[»]

ProteinModelPortal

P94692.

SMR

P94692. Positions 2-1232.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-29036N.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

InterPro

IPR001450. 4Fe4S-bd_dom.
IPR017896. 4Fe4S_Fe-S-bd.
IPR017900. 4Fe4S_Fe_S_CS.
IPR019456. Pyrv-flavodox_OxRtase_EKR.
IPR019752. Pyrv/ketoisovalerate_OxRed_cat.
IPR002880. Pyrv_Fd/Flavodoxin_OxRdtase_N.
IPR011895. Pyrv_flavodox_OxRed.
IPR002869. Pyrv_flavodox_OxRed_cen.
IPR011766. TPP_enzyme-bd_C.
IPR009014. Transketo_C/Pyr-ferredox_oxred.
IPR015941. Transketolase-like_C.
[Graphical view]

Gene3D

G3DSA:4.10.780.10. Pyrv-flavodox_OxRtase_EKR. 1 hit.
G3DSA:3.40.920.10. Pyrv_Fd/Flavodoxin_OxRdtase. 1 hit.
G3DSA:3.40.50.920. Transketo_C_like. 1 hit.

Pfam

PF10371. EKR. 1 hit.
PF00037. Fer4. 1 hit.
PF01558. POR. 1 hit.
PF01855. POR_N. 1 hit.
PF02775. TPP_enzyme_C. 1 hit.
[Graphical view]

PIRSF

PIRSF000159. NifJ. 1 hit.

SMART

SM00890. EKR. 1 hit.
[Graphical view]

SUPFAM

SSF53323. Pyrv_Fd/Flavodoxin_OxRdtase. 1 hit.
SSF52922. Transketo_C_like. 1 hit.

TIGRFAMs

TIGR02176. Pyruv_ox_red. 1 hit.

PROSITE

PS00198. 4FE4S_FER_1. 2 hits.
PS51379. 4FE4S_FER_2. 2 hits.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

P94692_DESAF

Accession

Primary (citable) accession number: P94692

Entry history

Integrated into UniProtKB/TrEMBL:	May 1, 1997
Last sequence update:	May 1, 1997
Last modified:	January 25, 2012
This is version 80 of the entry and version 1 of the sequence. [Complete history]

Entry status

Unreviewed (UniProtKB/TrEMBL)

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Regions

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Family and domain databases

Entry information