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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PGRP-IALPHAC IN COMPLEX WITH MURAMYL PENTAPEPTIDE
 
Authors :  R. Guan, A. Roychowdjury, G. Boons, R. A. Mariuzza
Date :  16 Aug 05  (Deposition) - 27 Jun 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Pgrps, Lys-Type, Peptidoglycan, Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Guan, P. H. Brown, C. P. Swaminathan, A. Roychowdhury, G. J. Boons, R. A. Mariuzza
Crystal Structure Of Human Peptidoglycan Recognition Protei I Alpha Bound To A Muramyl Pentapeptide From Gram-Positive Bacteria.
Protein Sci. V. 15 1199 2006
PubMed-ID: 16641493  |  Reference-DOI: 10.1110/PS.062077606

(-) Compounds

Molecule 1 - PEPTIDOGLYCAN RECOGNITION PROTEIN I-ALPHA
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System VectorPT7-7
    Expression System Vector TypePLASMID
    GenePGLYRP3, PGRPIA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPEPTIDOGLYCAN RECOGNITION PROTEIN INTERMEDIATE ALPHA, PGRP- I-ALPHA, PGLYRPIALPHA, PEPTIDOGLYCAN RECOGNITION PROTEIN 3
 
Molecule 2 - MURAMYL PENTAPEPTIDE
    ChainsC, D
    EngineeredYES
    Other DetailsMURAMYL PENTAPEPTIDE WAS SYNTHESIZED CHEMICALLY.
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D
Biological Unit 3 (1x)A (1x)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric Unit (5, 12)
No.NameCountTypeFull Name
1AMU2Mod. Amino AcidBETA-N-ACETYLMURAMIC ACID
2DAL4Mod. Amino AcidD-ALANINE
3GMA2Mod. Amino Acid4-AMIDO-4-CARBAMOYL-BUTYRIC ACID
4NH22Mod. Amino AcidAMINO GROUP
5SO42Ligand/IonSULFATE ION
Biological Unit 1 (5, 6)
No.NameCountTypeFull Name
1AMU1Mod. Amino AcidBETA-N-ACETYLMURAMIC ACID
2DAL2Mod. Amino AcidD-ALANINE
3GMA1Mod. Amino Acid4-AMIDO-4-CARBAMOYL-BUTYRIC ACID
4NH21Mod. Amino AcidAMINO GROUP
5SO41Ligand/IonSULFATE ION
Biological Unit 2 (5, 6)
No.NameCountTypeFull Name
1AMU1Mod. Amino AcidBETA-N-ACETYLMURAMIC ACID
2DAL2Mod. Amino AcidD-ALANINE
3GMA1Mod. Amino Acid4-AMIDO-4-CARBAMOYL-BUTYRIC ACID
4NH21Mod. Amino AcidAMINO GROUP
5SO41Ligand/IonSULFATE ION
Biological Unit 3 (5, 6)
No.NameCountTypeFull Name
1AMU1Mod. Amino AcidBETA-N-ACETYLMURAMIC ACID
2DAL2Mod. Amino AcidD-ALANINE
3GMA1Mod. Amino Acid4-AMIDO-4-CARBAMOYL-BUTYRIC ACID
4NH21Mod. Amino AcidAMINO GROUP
5SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:309 , HIS A:338 , HOH A:923 , HOH A:966BINDING SITE FOR RESIDUE SO4 A 900
2AC2SOFTWARESER B:334 , PHE B:339 , HIS B:341 , HOH B:943BINDING SITE FOR RESIDUE SO4 B 901

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:178 -A:300
2A:194 -A:238
3A:214 -A:220
4B:178 -B:300
5B:194 -B:238
6B:214 -B:220

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:199 -Pro A:200
2Ser A:324 -Pro A:325
3Leu B:199 -Pro B:200
4Ser B:324 -Pro B:325

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2APH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2APH)

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 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_HUMAN126-177522A:177-177
B:177-177
1
1
1.5ENST000002907225ENSE00001046175chr1:153275083-153274885199PGRP3_HUMAN177-243672A:177-243
B:177-243
67
67
1.6ENST000002907226ENSE00001046182chr1:153271707-153271589119PGRP3_HUMAN243-283412A:243-283
B:243-283
41
41
1.7ENST000002907227ENSE00001046177chr1:153270610-153270338273PGRP3_HUMAN283-341592A:283-341
B:283-341
59
59

(-) 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:165
 aligned with PGRP3_HUMAN | Q96LB9 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:165
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336     
         PGRP3_HUMAN    177 VCPNIIKRSAWEARETHCPKMNLPAKYVIIIHTAGTSCTVSTDCQTVVRNIQSFHMDTRNFCDIGYHFLVGQDGGVYEGVGWHIQGSHTYGFNDIALGIAFIGYFVEKPPNAAALEAAQDLIQCAVVEGYLTPNYLLMGHSDVVNILSPGQALYNIISTWPHFKH  341
               SCOP domains d2apha_ A: Peptidoglycan recognition protein I-alpha                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eee.....eee.................eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeeehhhhh.....hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1-----------------------------------------------------------------Exon 1.6  PDB: A:243-283 UniProt: 243-283---------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) Exon 1.5  PDB: A:177-243 UniProt: 177-243                          ---------------------------------------Exon 1.7  PDB: A:283-341 UniProt: 283-341                   Transcript 1 (2)
                2aph A  177 VCPNIIKRSAWEARETHCPKMNLPAKYVIIIHTAGTSCTVSTDCQTVVRNIQSFHMDTRNFCDIGYHFLVGQDGGVYEGVGWHIQGSHTYGFNDIALGIAFIGYFVEKPPNAAALEAAQDLIQCAVVEGYLTPNYLLMGHSDVVNILSPGQALYNIISTWPHFKH  341
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336     

Chain B from PDB  Type:PROTEIN  Length:165
 aligned with PGRP3_HUMAN | Q96LB9 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:165
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336     
         PGRP3_HUMAN    177 VCPNIIKRSAWEARETHCPKMNLPAKYVIIIHTAGTSCTVSTDCQTVVRNIQSFHMDTRNFCDIGYHFLVGQDGGVYEGVGWHIQGSHTYGFNDIALGIAFIGYFVEKPPNAAALEAAQDLIQCAVVEGYLTPNYLLMGHSDVVNILSPGQALYNIISTWPHFKH  341
               SCOP domains d2aphb_ B: Peptidoglycan recognition protein I-alpha                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eee.....eee.................eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeeehhhhh.....hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1-----------------------------------------------------------------Exon 1.6  PDB: B:243-283 UniProt: 243-283---------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) Exon 1.5  PDB: B:177-243 UniProt: 177-243                          ---------------------------------------Exon 1.7  PDB: B:283-341 UniProt: 283-341                   Transcript 1 (2)
                2aph B  177 VCPNIIKRSAWEARETHCPKMNLPAKYVIIIHTAGTSCTVSTDCQTVVRNIQSFHMDTRNFCDIGYHFLVGQDGGVYEGVGWHIQGSHTYGFNDIALGIAFIGYFVEKPPNAAALEAAQDLIQCAVVEGYLTPNYLLMGHSDVVNILSPGQALYNIISTWPHFKH  341
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336     

Chain C from PDB  Type:PROTEIN  Length:7
                                        
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                2aph C  883 xAeKaax  889
                            | | |||
                          883-AMU||
                            885-GMA
                              887-DAL
                               888-DAL
                                889-NH2

Chain D from PDB  Type:PROTEIN  Length:7
                                        
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                2aph D  994 xAeKaax 1000
                            | | |||
                            | | |||
                          994-AMU||
                            996-GMA
                              998-DAL
                               999-DAL
                               1000-NH2

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2APH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2APH)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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 1sk4 1twq

(-) Related Entries Specified in the PDB File

1twq THE SAME PROTEIN IN COMPLEX WITH ANOTHER LIGAND
1sk3 THE SAME PROTEIN IN FREE FORM
1sk4 THE SAME PROTEIN IN FREE FORM