2I45,3D82


Conserved Protein Domain Family
cupin_YdbB-like
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cd02226: cupin_YdbB-like 
Bacillus subtilis YdbB and related proteins, cupin domain
This family includes bacterial proteins homologous to YdbB, a Bacillus subtilis protein of unknown function. It also includes protein Nmb1881 From Neisseria meningitidis, also of unknown function. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.
Links
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Statistics
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PSSM-Id: 380355
Aligned: 153 rows
Threshold Bit Score: 108.683
Created: 3-Oct-2005
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
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metal bindingputative active
Conserved site includes 4 residues -Click on image for an interactive view with Cn3D
Feature 1: metal binding site [ion binding site], 4 residue positions
Conserved feature residue pattern:[QH] [NH] E HClick to see conserved feature residue pattern help
Evidence:
  • Structure:3D82: Shewanella frigidimarina YdbB binds Ni2+; contacts at 4.0A
  • Comment:The four-coordinate metallocenter usually includes three histidines and one glutamate.
  • Citation:PMID 8612079
Download Cn3D for Viewing 3D StructureScroll to Sequence Alignment Display
Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
Feature 1                                             # #    #                                   
2I45_A         7 NLKQHLAAikeYWQPEIINrh-gFQFHLVKLLGDYgWHTHGYsDKVLFAVEGDXAVDFadgGSXTIRe--GEXAVVPkSV 83  Neisseria menin...
3D82_A         8 NFNDKFSLfnqHWSPRVIAexndYQFKLVKVEGEFvWHEHADtDEVFIVXEGTLQIAFr-dQNITLQa--GEXYVIPkGV 84  Shewanella frig...
WP_067684337   6 SLADKFATfseTWAPRIVAryegHEVRIARLDGEFdWHAHDH-DELFLCLDGTLDVEFr-dRTETLGp--GELLLIGkGE 81  Erythrobacter s...
WP_092062880   9 NAFDLTKDitdDWKNFVVSeindHVVRLSVLQRDFhWHYHAEsDEMFYVIEGKLFVDLe-dRTEELNp--GEMITIPkNV 85  Desulfonauticus...
WP_018154671  12 DVSELTKDindDWKNFVVSeindHVVRLSVLQRDFhWHLHKNsDEFFYVIEGKLFVDFe-dRTEEIGp--GQMITIPkNV 88  Methanothermoco...
WP_018123273  11 SLLELTNKveeDWKSLRVAtindQDIRVSILQREFhWHTHNDsDEAFYVIQGCLEVDFe-dRTETLGp--GDLLVVPcGT 87  Desulfovibrio o...
PIE22894       9 DLLDVFAQieePWKPELIAslngQALRAALFEGEFvWHKPDEeDELFFVVQGECELQF---RDHSLQlsgGQLCVVPkGT 85  Planctomycetes ...
OGQ77423       5 DIPREIAEh-ePWFNQTLTtvndAVVRLGIFDGEFhWHKHDEqDEMFLVLKGRLFLDVegrGSVELTa--HQAYTVPkGV 81  Deltaproteobact...
OJW54296      22 DINRMINEctdKWFNQTLTkvndSVVRIGIVEGEYhWHKHDNdDEFFYVLQGQLLVDLe-dRTIELNp--NEGVTIPkGV 98  Sphingobacteria...
ABZ82945       3 DIPALVSActeKWMNMAVSqvndAVIRLGVIEGEFhWHKHDReDEFFFVVSGKLFIDLe-dRTVVLLp--QQGYTVPlGV 79  Heliobacterium ...

Feature 1         #                
2I45_A        84 SHRPRSen-gCSLVLIEL 100 Neisseria meningitidis
3D82_A        85 EHKPXAke-eCKIXIIEP 101 Shewanella frigidimarina NCIMB 400
WP_067684337  82 DHRPVAsrgeVRLLMLDP 99  Erythrobacter sp. HI0063
WP_092062880  86 KHRTRSse-rTLILCFES 102 Desulfonauticus submarinus
WP_018154671  89 RHRTRSnq-rTVILCFES 105 Methanothermococcus thermolithotrophicus
WP_018123273  88 LHRTRSnl-rTVSICFTA 104 Desulfovibrio oxyclinae
PIE22894      86 LHRAVAke-pCLMLLLEP 102 Planctomycetes bacterium
OGQ77423      82 KHRPRSpa-kSVVLMIEQ 98  Deltaproteobacteria bacterium RIFOXYA12_FULL_58_15
OJW54296      99 IHRTRApk-kTVMLMVET 115 Sphingobacteriales bacterium 50-39
ABZ82945      80 LHRTRApe-rTVILMVEK 96  Heliobacterium modesticaldum Ice1

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