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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL PEPTIDOGLYCAN-BINDING DOMAIN OF HUMAN PEPTIDOGLYCAN RECOGNITION PROTEIN IALPHA
 
Authors :  R. Guan, E. L. Malchiodi, W. Qian, P. Schuck, R. A. Mariuzza
Date :  04 Mar 04  (Deposition) - 13 Jul 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Alpha/Beta Mix, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Guan, E. L. Malchiodi, W. Qian, P. Schuck, R. A. Mariuzza
Crystal Structure Of The C-Terminal Peptidoglycan-Binding Domain Of Human Peptidoglycan Recognition Protein Ialpha
J. Biol. Chem. V. 279 31873 2004
PubMed-ID: 15140887  |  Reference-DOI: 10.1074/JBC.M404920200

(-) Compounds

Molecule 1 - PEPTIDOGLYCAN RECOGNITION PROTEIN I-ALPHA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPT7-7
    Expression System StrainBL21 DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GenePGRPIA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPEPTIDOGLYCAN RECOGNITION PROTEIN INTERMEDIATE ALPHA, PGRP- I-ALPHA, PGLYRPIALPHA

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
2NA1Ligand/IonSODIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CSO2Mod. Amino AcidS-HYDROXYCYSTEINE
2NA-1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:36 , SER A:317 , ASP A:318 , VAL A:319 , ILE A:322 , SER A:324 , GLN A:327BINDING SITE FOR RESIDUE NA A 342

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:194 -A:238
2A:214 -A:220

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:199 -Pro A:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SK4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SK4)

(-) Exons   (3, 3)

Asymmetric Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002907221ENSE00001072539chr1:153283194-153283087108PGRP3_HUMAN1-19190--
1.2ENST000002907222ENSE00001072538chr1:153279743-153279542202PGRP3_HUMAN19-86680--
1.3ENST000002907223ENSE00001615390chr1:153277541-153277423119PGRP3_HUMAN86-126410--
1.4ENST000002907224ENSE00001046162chr1:153276485-153276333153PGRP3_HUMAN126-177520--
1.5ENST000002907225ENSE00001046175chr1:153275083-153274885199PGRP3_HUMAN177-243671A:179-24365
1.6ENST000002907226ENSE00001046182chr1:153271707-153271589119PGRP3_HUMAN243-283411A:243-28341
1.7ENST000002907227ENSE00001046177chr1:153270610-153270338273PGRP3_HUMAN283-341591A:283-34159

(-) 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:163
 aligned with PGRP3_HUMAN | Q96LB9 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:163
                                   188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338   
          PGRP3_HUMAN   179 PNIIKRSAWEARETHCPKMNLPAKYVIIIHTAGTSCTVSTDCQTVVRNIQSFHMDTRNFCDIGYHFLVGQDGGVYEGVGWHIQGSHTYGFNDIALGIAFIGYFVEKPPNAAALEAAQDLIQCAVVEGYLTPNYLLMGHSDVVNILSPGQALYNIISTWPHFKH 341
               SCOP domains d1sk4a_ A: Peptidoglycan recognition protein I-alpha                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------Amidase_2-1sk4A01 A:192-328                                                                                                              ------------- Pfam domains (1)
           Pfam domains (2) -------------Amidase_2-1sk4A02 A:192-328                                                                                                              ------------- Pfam domains (2)
         Sec.struct. author ....hhhhhh............eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eee.....eee.................eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeee.hhh.......hhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5  PDB: A:179-243 UniProt: 177-243 [INCOMPLETE]           ---------------------------------------Exon 1.7  PDB: A:283-341 UniProt: 283-341                   Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------Exon 1.6  PDB: A:243-283 UniProt: 243-283---------------------------------------------------------- Transcript 1 (2)
                 1sk4 A 179 PNIIKRSAWEARETHCPKMNLPAKYVIIIHTAGTSCTVSTDCQTVVRNIQSFHMDTRNFCDIGYHFLVGQDGGVYEGVGWHIQGSHTYGFNDIALGIAFIGYFVEKPPNAAALEAAQDLIQcAVVEGYLTPNYLLMGHSDVVNILSPGQALYNIISTWPHFKH 341
                                   188       198       208       218       228       238       248       258       268       278       288       298 |     308       318       328       338   
                                                                                                                                                   300-CSO                                     

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 1SK4)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A   (PGRP3_HUMAN | Q96LB9)
molecular function
    GO:0008745    N-acetylmuramoyl-L-alanine amidase activity    Catalysis of the hydrolysis of the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides.
    GO:0042834    peptidoglycan binding    Interacting selectively and non-covalently, in a non-covalent manner, with peptidoglycan, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0016019    peptidoglycan receptor activity    Combining with a peptidoglycan and transmitting the signal to initiate a change in cell activity.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0050830    defense response to Gram-positive bacterium    Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0016045    detection of bacterium    The series of events in which a stimulus from a bacterium is received and converted into a molecular signal.
    GO:0044117    growth of symbiont in host    The increase in size or mass of an organism, occurring within the cells or tissues of the host organism. This may (but not necessarily) include a filamentous growth form, and also can include secretion of proteases and lipases to break down host tissue. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0032689    negative regulation of interferon-gamma production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
    GO:0032827    negative regulation of natural killer cell differentiation involved in immune response    Any process that stops, prevents, or reduces the frequency, rate or extent of natural killer cell differentiation as part of an immune response.
    GO:0002221    pattern recognition receptor signaling pathway    Any series of molecular signals generated as a consequence of a pattern recognition receptor (PRR) binding to one of its physiological ligands. PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved among microbial species, or damage-associated molecular pattern (DAMPs), endogenous molecules released from damaged cells.
    GO:0009253    peptidoglycan catabolic process    The chemical reactions and pathways resulting in the breakdown of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
cellular component
    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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PGRP3_HUMAN | Q96LB91sk3 1twq 2aph

(-) Related Entries Specified in the PDB File

1oht PEPTIDOGLYCAN RECOGNITION PROTEIN-LB
1sk3 CRYSTAL STRUCTURE OF THE C-TERMINAL PEPTIDOGLYCAN-BINDING DOMAIN OF HUMAN PEPTIDOGLYCAN RECOGNITION PROTEIN IALPHA