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Protein

Biosynthetic arginine decarboxylase

Gene

speA

Organism
Vibrio vulnificus (strain YJ016)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the biosynthesis of agmatine from arginine.UniRule annotation

Catalytic activityi

L-arginine = agmatine + CO2.UniRule annotation

Cofactori

Protein has several cofactor binding sites:
  • Mg2+UniRule annotation
  • pyridoxal 5'-phosphateUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Polyamine biosynthesis, Spermidine biosynthesis

Keywords - Ligandi

Magnesium, Metal-binding, Pyridoxal phosphate

Enzyme and pathway databases

BRENDAi4.1.1.19. 7786.

Names & Taxonomyi

Protein namesi
Recommended name:
Biosynthetic arginine decarboxylaseUniRule annotation (EC:4.1.1.19UniRule annotation)
Short name:
ADCUniRule annotation
Gene namesi
Name:speAUniRule annotation
Ordered Locus Names:VV1986
OrganismiVibrio vulnificus (strain YJ016)
Taxonomic identifieri196600 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
Proteomesi
  • UP000002675 Componenti: Chromosome I

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001499861 – 640Biosynthetic arginine decarboxylaseAdd BLAST640

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei105N6-(pyridoxal phosphate)lysineUniRule annotation1

Structurei

Secondary structure

1640
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi11 – 18Combined sources8
Helixi21 – 24Combined sources4
Beta strandi27 – 30Combined sources4
Beta strandi36 – 38Combined sources3
Helixi50 – 59Combined sources10
Beta strandi64 – 69Combined sources6
Helixi71 – 92Combined sources22
Beta strandi98 – 100Combined sources3
Helixi104 – 106Combined sources3
Helixi110 – 122Combined sources13
Beta strandi129 – 132Combined sources4
Helixi135 – 144Combined sources10
Beta strandi146 – 148Combined sources3
Beta strandi151 – 154Combined sources4
Helixi160 – 171Combined sources12
Beta strandi175 – 180Combined sources6
Helixi185 – 196Combined sources12
Beta strandi201 – 206Combined sources6
Turni213 – 216Combined sources4
Beta strandi218 – 221Combined sources4
Helixi230 – 242Combined sources13
Helixi246 – 248Combined sources3
Beta strandi249 – 253Combined sources5
Beta strandi258 – 260Combined sources3
Helixi263 – 282Combined sources20
Beta strandi289 – 291Combined sources3
Helixi315 – 333Combined sources19
Beta strandi339 – 342Combined sources4
Helixi345 – 349Combined sources5
Helixi350 – 352Combined sources3
Beta strandi353 – 363Combined sources11
Helixi379 – 389Combined sources11
Helixi397 – 419Combined sources23
Helixi425 – 445Combined sources21
Helixi453 – 463Combined sources11
Beta strandi466 – 472Combined sources7
Helixi474 – 477Combined sources4
Helixi479 – 484Combined sources6
Beta strandi490 – 494Combined sources5
Helixi496 – 498Combined sources3
Beta strandi501 – 511Combined sources11
Beta strandi520 – 522Combined sources3
Beta strandi525 – 532Combined sources8
Beta strandi542 – 547Combined sources6
Helixi552 – 555Combined sources4
Helixi559 – 561Combined sources3
Beta strandi566 – 572Combined sources7
Beta strandi578 – 584Combined sources7
Helixi589 – 595Combined sources7
Helixi600 – 614Combined sources15
Helixi617 – 632Combined sources16
Beta strandi633 – 636Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3N2OX-ray2.30A/B/C/D1-640[»]
ProteinModelPortaliQ7MK24.
SMRiQ7MK24.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ7MK24.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni290 – 300Substrate-bindingUniRule annotationAdd BLAST11

Sequence similaritiesi

Belongs to the Orn/Lys/Arg decarboxylase class-II family. SpeA subfamily.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000029191.
KOiK01585.
OMAiDQLFPIM.
OrthoDBiPOG091H04NG.

Family and domain databases

CDDicd06830. PLPDE_III_ADC. 1 hit.
Gene3Di2.40.37.10. 2 hits.
3.20.20.10. 1 hit.
HAMAPiMF_01417. SpeA. 1 hit.
InterProiIPR009006. Ala_racemase/Decarboxylase_C.
IPR002985. Arg_decrbxlase.
IPR022643. De-COase2_C.
IPR022644. De-COase2_N.
IPR000183. Orn/DAP/Arg_de-COase.
IPR029066. PLP-binding_barrel.
[Graphical view]
PANTHERiPTHR11482:SF36. PTHR11482:SF36. 2 hits.
PfamiPF02784. Orn_Arg_deC_N. 1 hit.
PF00278. Orn_DAP_Arg_deC. 1 hit.
[Graphical view]
PIRSFiPIRSF001336. Arg_decrbxlase. 1 hit.
PRINTSiPR01180. ARGDCRBXLASE.
PR01179. ODADCRBXLASE.
SUPFAMiSSF51419. SSF51419. 1 hit.
TIGRFAMsiTIGR01273. speA. 1 hit.

Sequencei

Sequence statusi: Complete.

Q7MK24-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRLDVEQTSK LDRVRADYNV HYWSQGFYGI DDQGEMYVSP RSDNAHQIQL
60 70 80 90 100
SKIVKQLEER QLNVPVLVRF PQILHQRVHS ICDAFNQAIE EYQYPNKYLL
110 120 130 140 150
VYPIKVNQQR EVVDEILASQ AQLETKQLGL EAGSKPELLA VLAMAQHASS
160 170 180 190 200
VIVCNGYKDR EYIRLALIGE KLGHKVFIVL EKMSELDLVL REAKSLGVTP
210 220 230 240 250
RLGIRIRLAS QGAGKWQASG GEKSKFGLSA SQVLNVISRL KKENQLDTLQ
260 270 280 290 300
LVHFHLGSQM ANIRDVRNGV NESARFYCEL RTLGANITYF DVGGGLAIDY
310 320 330 340 350
DGTRSQSSNS MNYGLVEYAR NIVNTVGDVC KDYKQPMPVI ISESGRSLTA
360 370 380 390 400
HHAVLISNVI GTETYKPETV TEPEEDFPLL LNNMWRSWLN LHNGTDARAL
410 420 430 440 450
IEIYNDTQSD LAEVHSQFAT GVLTLEHRAW AEQTSLRIYY ELNRLMSTKN
460 470 480 490 500
RFHRPILDEL SERLADKFFV NFSLFQSLPD SWGIDQVFPV LPLSGLQNAA
510 520 530 540 550
DRRAVMLDIT CDSDGAIDAY VDGQGIESTL PVPAWNEDEP YLMGFFLVGA
560 570 580 590 600
YQEILGDMHN LFGDTHSVVV NVGDQGEINI DFINEGDTVE DMMRYVHIDV
610 620 630 640
DQIRKNYHSL VSQRVDQEEQ QQILAELEQG LSGYTYLEDF
Length:640
Mass (Da):72,493
Last modified:December 15, 2003 - v1
Checksum:i3157EA5825FFF912
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000037 Genomic DNA. Translation: BAC94750.1.

Genome annotation databases

EnsemblBacteriaiBAC94750; BAC94750; BAC94750.
KEGGivvy:VV1986.
PATRICi20170858. VBIVibVul40472_2014.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000037 Genomic DNA. Translation: BAC94750.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3N2OX-ray2.30A/B/C/D1-640[»]
ProteinModelPortaliQ7MK24.
SMRiQ7MK24.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC94750; BAC94750; BAC94750.
KEGGivvy:VV1986.
PATRICi20170858. VBIVibVul40472_2014.

Phylogenomic databases

HOGENOMiHOG000029191.
KOiK01585.
OMAiDQLFPIM.
OrthoDBiPOG091H04NG.

Enzyme and pathway databases

BRENDAi4.1.1.19. 7786.

Miscellaneous databases

EvolutionaryTraceiQ7MK24.

Family and domain databases

CDDicd06830. PLPDE_III_ADC. 1 hit.
Gene3Di2.40.37.10. 2 hits.
3.20.20.10. 1 hit.
HAMAPiMF_01417. SpeA. 1 hit.
InterProiIPR009006. Ala_racemase/Decarboxylase_C.
IPR002985. Arg_decrbxlase.
IPR022643. De-COase2_C.
IPR022644. De-COase2_N.
IPR000183. Orn/DAP/Arg_de-COase.
IPR029066. PLP-binding_barrel.
[Graphical view]
PANTHERiPTHR11482:SF36. PTHR11482:SF36. 2 hits.
PfamiPF02784. Orn_Arg_deC_N. 1 hit.
PF00278. Orn_DAP_Arg_deC. 1 hit.
[Graphical view]
PIRSFiPIRSF001336. Arg_decrbxlase. 1 hit.
PRINTSiPR01180. ARGDCRBXLASE.
PR01179. ODADCRBXLASE.
SUPFAMiSSF51419. SSF51419. 1 hit.
TIGRFAMsiTIGR01273. speA. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiSPEA_VIBVY
AccessioniPrimary (citable) accession number: Q7MK24
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 29, 2004
Last sequence update: December 15, 2003
Last modified: November 2, 2016
This is version 79 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.