5F6Z


Conserved Protein Domain Family
lipocalin_apoD-like

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cd19437: lipocalin_apoD-like 
apolipoprotein D and similar proteins
Human apolipoprotein D (ApoD) is a small glycoprotein associated with high density lipoproteins (HDL) in plasma. It appears promiscuous since it can bind hydrophobic ligands belonging to different lipid groups, with different shapes and biochemical properties; however, it exhibits specificity between very similar lipidic species. Some ligands, such as progesterone and arachidonic acid, bind to the ligand-binding pocket with high affinity, while others may interact with ApoD via its region of surface hydrophobicity. This hydrophobic surface cluster may facilitate its association with HDL particles and facilitate its insertion into cellular lipid membranes. Drosophila NLaz and Schistocerca Laz belong to this group, and share functional properties with human ApoD, including regulation of lifespan, lipid and carbohydrate metabolism control, and protection against oxidative stress or starvation. This group also includes Sandercyanin, a blue protein secreted in the skin mucus of blue forms of walleye, Sander vitreus. Walleye is an important golden yellow commercial and sport fish; the findings of blue walleye are recent. This group belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development.
Statistics
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PSSM-Id: 381212
Aligned: 41 rows
Threshold Bit Score: 182.06
Created: 7-Feb-2006
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
ligand binding
Conserved site includes 31 residues -Click on image for an interactive view with Cn3D
Feature 1:ligand binding cavity [chemical binding site]
Evidence:
  • Comment:hydrophobic cavity binds different hydrophobic ligands; ligands are bound within the beta-barrel in a central internal water-filled cavity lined with polar and hydrophobic amino acids
  • Comment:based on Sander vitreus sandercyanin and on other lipocalin/cytosolic fatty-acid binding protein family members with structure
  • Structure:5F6Z; Sander vitreus sandercyanin homotetramer bound with biliverdine IX alpha; contacts at 4A
  • Comment:Sandercyanin is a monomeric protein that forms stable homotetramers upon addition of Biliverdin IX alpha to the protein
  • Structure:27688756

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                         #   #          ##      ### #        # # ####       # #  # #    
5F6Z_A         5 PGRCPKPAVQeDFDAARYLGVWYDIQRL-PNKFQk--gECATATYSLSPg-VGFSVFNRERLa-NGTIKSVI-GSAIAEd 78  walleye
EJY70703      22 FGSCPKVDTVeNFDAEKYTGRWYEINRDrQTPFEkr-gTCVTADYSLGDaeSTIKVRNSMFR--DGSQQTTE-GTATCEg 97  Oxytricha trifa...
EJY67928      24 FGSCPTLKLQdNFDATKYIGVWYEQSRDkAIPFEh--fDCNQALYGLIQ--TGLSVHNTEFNnqTGMIQSAI-GTASCNg 98  Oxytricha trifa...
XP_002609575  23 GDSCPRVPTKeNFDIVPYMGRWYELSKY-PNSFQn--gECGTAIYRLEAd-NTVTVNNTQIKd-DGSSDTVI-GQARDDp 96  Florida lancelet
EJY69374      24 LGACPKPQLQqDFDINRYLGAWFEQARDhSIPWEh--gTCPQARYQLKDdgLSLAVINSEYNekTGEVEIAP-ANATCNg 100 Oxytricha trifa...
EJY70216      22 LGKCKTVKLMeNFDALKYQGTWYEQARDkGMVFEs--yDCQQARYNIYNd-GVLRVHNTQFNp-NGTIESAF-ANGTCNg 96  Oxytricha trifa...
EJY67927      26 TGSCTTPQLQeKFDAQRYTGRWYEVRRD-NGQFGendyDCENAIYTLNTd-GTLHVKNSGFSltNQTYFDVE-GDATCVg 102 Oxytricha trifa...
EJY70703     382 LGLCDNPNLVqNFDVAKYAGVWYEIYRDsETPFEkn-sKCVTANYGLNRd-NTLSVYNRGVEstDNSVMDVS-GFASCIn 458 Oxytricha trifa...
EJY71744      24 WGKCPNFHVQsDFDLNNYAGQWFEQARDiDTFYEk--gDCVHGKYVVDDe-GFMRITNAQFDl-EKREHTIAeGRAICTg 99  Oxytricha trifa...
EJY76322      33 LGKCPEVQLRsTLDTALYKGRWYEVQRG-DLFQEdd-qICVTADYTLQYd-RSLRIKNRARYp-DGSFGGIM-GRVVCRq 107 Oxytricha trifa...
Feature 1               # # #         # # #        # # #   #        # # #                        
5F6Z_A        79 pc-epAKLQFFHENa----APVPYWVLSTDYDNYALVYSCINLg--aSHAAYASIVSRQpt-lpEETIKKLQGTMSSf-- 148 walleye
EJY70703      98 -----SRCLVSFGPy---aPAGKYWVIDTDYENFSIVYSCTDYmmsmYKTEYLWVLARDnkfdsTEVLEKVKSTIEG--- 166 Oxytricha trifa...
EJY67928      99 -----AQCQVQFNPk---aPAGDYRVLSTDYDNYSIVYSCVDIfg-fSKVQFIWLLTRTpe-lsQEVLQNAKQIIKTevp 168 Oxytricha trifa...
XP_002609575  97 dsdipGRLQVRFSSf---qPWGSYWVVDTDYDNYSIVYSCNYFl--vNRVEFLWILARDra-lpAGTMSSILQKIESy-- 168 Florida lancelet
EJY69374     101 -----PACKVKFNNn---lPQGDYRVLSTDYDNYAVVYSCTDVfg-fSKVEFVWILTRQqe-vtDEVATTIHQKLSEgvp 170 Oxytricha trifa...
EJY70216      97 -----AQCGIKFEQqptwtPKGDYRVLDTDYESYSVVYSCSDVlg-fGKFHYVWVLTRDqv-isEAIKVKATSILQErvp 169 Oxytricha trifa...
EJY67927     103 -----PQCTVVFFN-----RPADYRVLYTDYDNFGIVYSCTDLeg-lAKFEGVWVLSRTkt-atDDQVNKVLSILSErvp 170 Oxytricha trifa...
EJY70703     459 n---eANCEVQFNFf----ARGDYRVISTDYDKYSLVFSCSSYy--lFKNEFFWILSKQrt-idDSLLQEIKGIMEIevp 528 Oxytricha trifa...
EJY71744     100 -----AYCYSRFHNmi--dLFGDYQILSTDYSKYAIVYTCSNFld-vFSNDKVWLLTREan-vsQEVLSEIHETLWKqhs 170 Oxytricha trifa...
EJY76322     108 -----AECRAKFDQff--iPAGKYMVLDTDYNTYAIVYTCAQYlfgvFKQENVWVLSRSttafdATTQTNILNTIQTrip 180 Oxytricha trifa...
Feature 1                    
5F6Z_A       149 gVGVDTLLTTNQ 160 walleye
EJY70703     167 -YDVGFLMETVQ 177 Oxytricha trifallax
EJY67928     169 dYTFDNFHVTKQ 180 Oxytricha trifallax
XP_002609575 169 gIDSTKLVDTVQ 180 Florida lancelet
EJY69374     171 kYNQSVISRNHH 182 Oxytricha trifallax
EJY70216     170 eYSFDNFRITKQ 181 Oxytricha trifallax
EJY67927     171 eYNLEALLSPRQ 182 Oxytricha trifallax
EJY70703     529 rYQFESLLKTDQ 540 Oxytricha trifallax
EJY71744     171 dYGKRNFYYTQQ 182 Oxytricha trifallax
EJY76322     181 nYDITKLKTTPQ 192 Oxytricha trifallax

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