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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE APOLIPOPROTEIN A-I BINDING PROTEIN IN COMPLEX WITH THYMINE.
 
Authors :  I. A. Shumilin, K. N. Jha, M. Cymborowski, J. C. Herr, W. Minor
Date :  25 Apr 11  (Deposition) - 18 Jul 12  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (2x)
Biol. Unit 3:  A  (6x)
Keywords :  Rossmann Fold, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. A. Shumilin, M. Cymborowski, O. Chertihin, K. N. Jha, J. C. Herr, S. A. Lesley, A. Joachimiak, W. Minor
Identification Of Unknown Protein Function Using Metabolite Cocktail Screening.
Structure V. 20 1715 2012
PubMed-ID: 22940582  |  Reference-DOI: 10.1016/J.STR.2012.07.016

(-) Compounds

Molecule 1 - APOLIPOPROTEIN A-I-BINDING PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21A
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneAIBP, APOA1BP
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymAI-BP

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A
Biological Unit 2 (2x)A
Biological Unit 3 (6x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION
3TDR1Ligand/IonTHYMINE
Biological Unit 1 (3, 16)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION
3TDR2Ligand/IonTHYMINE
Biological Unit 2 (3, 16)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION
3TDR2Ligand/IonTHYMINE
Biological Unit 3 (3, 48)
No.NameCountTypeFull Name
1MSE36Mod. Amino AcidSELENOMETHIONINE
2SO46Ligand/IonSULFATE ION
3TDR6Ligand/IonTHYMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:35 , ASP A:39 , ASP A:188 , LEU A:211 , LYS A:215BINDING SITE FOR RESIDUE TDR A 300
2AC2SOFTWAREGLY A:88 , ASN A:89 , ASN A:90 , GLY A:159 , SER A:161 , HOH A:286BINDING SITE FOR RESIDUE SO4 A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RO7)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:77 -Pro A:78
2Lys A:163 -Gly A:164
3Gly A:164 -Asp A:165
4Glu A:168 -Pro A:169

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RO7)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1YJEF_NPS51385 YjeF N-terminal domain profile.NNRE_MOUSE59-269  1A:35-245
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1YJEF_NPS51385 YjeF N-terminal domain profile.NNRE_MOUSE59-269  2A:35-245
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1YJEF_NPS51385 YjeF N-terminal domain profile.NNRE_MOUSE59-269  2A:35-245
Biological Unit 3 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1YJEF_NPS51385 YjeF N-terminal domain profile.NNRE_MOUSE59-269  6A:35-245

(-) Exons   (0, 0)

(no "Exon" information available for 3RO7)

(-) Sequences/Alignments

Asymmetric 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:233
 aligned with NNRE_MOUSE | Q8K4Z3 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:233
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279   
           NNRE_MOUSE    50 AVKYLSQEEAQAVDQELFNEYQFSVDQLMELAGLSCATAIAKAYPPTSMSKSPPTVLVICGPGNNGGDGLVCARHLKLFGYQPTIYYPKRPNKPLFTGLVTQCQKMDIPFLGEMPPEPMMVDELYELVVDAIFGFSFKGDVREPFHSILSVLSGLTVPIASIDIPSGWDVEKGNPSGIQPDLLISLTAPKKSATHFTGRYHYLGGRFVPPALEKKYQLNLPSYPDTECVYRLQ 282
               SCOP domains d3ro7a_ A: automated matches                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhh..........hhhhhhhhh.eeeee............hhhhhhhhhh.....eeee...................eeeee...hhhhhhh...eeeee....hhhhhhhh............eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------YJEF_N  PDB: A:35-245 UniProt: 59-269                                                                                                                                                                              ------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ro7 A  26 AVKYLSQEEAQAVDQELFNEYQFSVDQLmELAGLSCATAIAKAYPPTSmSKSPPTVLVICGPGNNGGDGLVCARHLKLFGYQPTIYYPKRPNKPLFTGLVTQCQKmDIPFLGEmPPEPmmVDELYELVVDAIFGFSFKGDVREPFHSILSVLSGLTVPIASIDIPSGWDVEKGNPSGIQPDLLISLTAPKKSATHFTGRYHYLGGRFVPPALEKKYQLNLPSYPDTECVYRLQ 258
                                    35        45        55        65        75        85        95       105       115       125     | 135   |   145       155       165       175       185       195       205       215       225       235       245       255   
                                                       54-MSE              74-MSE                                                  131-MSE 139-MSE||                                                                                                                 
                                                                                                                                                144-MSE                                                                                                              
                                                                                                                                                 145-MSE                                                                                                             

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RO7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3RO7)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A   (NNRE_MOUSE | Q8K4Z3)
molecular function
    GO:0052856    NADHX epimerase activity    Catalysis of the reaction: (R)-NADHX = (S)-NADHX.
    GO:0052857    NADPHX epimerase activity    Catalysis of the reaction: (R)-NADPHX = (S)-NADPHX.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
cellular component
    GO:0044297    cell body    The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
    GO:0005929    cilium    A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NNRE_MOUSE | Q8K4Z32dg2 2o8n 3rno 3roe 3rog 3rox 3roz

(-) Related Entries Specified in the PDB File

2dg2 APO-PROTEIN
2o8n APO-PROTEIN
3rno
3roe
3rog
3rox
3roz