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(-) Description

Title :  COMPLEMENT COMPONENT C2A
 
Authors :  F. J. Milder, H. C. A. Raaijmakers, D. A. A. Vandeputte, A. Schouten, E. G. Huizinga, R. A. Romijn, W. Hemrika, A. Roos, M. R. Daha, P. Gros
Date :  29 Aug 06  (Deposition) - 17 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Serine Protease Domain, Von Willebrand Factor-A Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. J. Milder, H. C. Raaijmakers, M. D. Vandeputte, A. Schouten, E. G. Huizinga, R. A. Romijn, W. Hemrika, A. Roos, M. R. Daha, P. Gros
Structure Of Complement Component C2A: Implications For Convertase Formation And Substrate Binding.
Structure V. 14 1587 2006
PubMed-ID: 17027507  |  Reference-DOI: 10.1016/J.STR.2006.08.008

(-) Compounds

Molecule 1 - COMPLEMENT C2A FRAGMENT
    ChainsA
    EC Number3.4.21.43
    EngineeredYES
    Expression SystemMESOCRICETUS AURATUS
    Expression System CommonGOLDEN HAMSTER
    Expression System PlasmidPNUT
    Expression System Taxid10036
    Expression System Vector TypePLASMID
    GeneC2A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2FUC1Ligand/IonALPHA-L-FUCOSE
3MLI1Ligand/IonMALONATE ION
4MN1Ligand/IonMANGANESE (II) ION
5NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:312 , ASN A:313 , VAL A:702 , NAG A:1314 , FUC A:1315BINDING SITE FOR RESIDUE NAG A 1313
2AC2SOFTWAREGLN A:624 , VAL A:702 , PRO A:704 , NAG A:1313 , NAG A:1314BINDING SITE FOR RESIDUE FUC A 1315
3AC3SOFTWARENAG A:1313 , FUC A:1315BINDING SITE FOR RESIDUE NAG A 1314
4AC4SOFTWAREHOH A:1 , HOH A:7 , HOH A:193 , LYS A:224 , GLU A:430 , HIS A:431 , LEU A:433 , VAL A:435 , ASN A:447 , ALA A:452 , GLU A:456 , NAG A:1448BINDING SITE FOR RESIDUE NAG A 1447
5AC5SOFTWARELYS A:224 , HIS A:431 , ASP A:434 , NAG A:1447 , BMA A:1449BINDING SITE FOR RESIDUE NAG A 1448
6AC6SOFTWARENAG A:1448BINDING SITE FOR RESIDUE BMA A 1449
7AC7SOFTWAREASN A:601 , ARG A:694 , ARG A:696BINDING SITE FOR RESIDUE NAG A 1601
8AC8SOFTWARESER A:242 , SER A:244 , THR A:317 , HOH A:1002 , HOH A:1003 , MLI A:1004BINDING SITE FOR RESIDUE MN A 1001
9AC9SOFTWAREHOH A:56 , HOH A:194 , SER A:242 , GLN A:243 , SER A:244 , THR A:315 , GLY A:316 , THR A:317 , ASN A:360 , VAL A:519 , PRO A:522 , TRP A:718 , HIS A:722 , MN A:1001 , HOH A:1003BINDING SITE FOR RESIDUE MLI A 1004

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:443 -A:561
2A:472 -A:488
3A:564 -A:580
4A:618 -A:645
5A:655 -A:685

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:702 -Pro A:703

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_019158E318DCO2_HUMANPolymorphism9332739AE298D
2UniProtVAR_008546G464RCO2_HUMANDisease (C2D)151340617AG444R
3UniProtVAR_011772F533LCO2_HUMANPolymorphism1042664AF513L
4UniProtVAR_019159R734CCO2_HUMANPolymorphism4151648AR714C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (4, 4)

Asymmetric/Biological Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VWFAPS50234 VWFA domain profile.CO2_HUMAN254-452  1A:234-432
2TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.CO2_HUMAN464-744  1A:444-724
3TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.CO2_HUMAN503-508  1A:483-488
4TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.CO2_HUMAN673-684  1A:653-664

(-) Exons   (0, 0)

(no "Exon" information available for 2I6Q)

(-) Sequences/Alignments

Asymmetric/Biological 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:503
 aligned with CO2_HUMAN | P06681 from UniProtKB/Swiss-Prot  Length:752

    Alignment length:510
                                   252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752
            CO2_HUMAN   243 RKIQIQRSGHLNLYLLLDCSQSVSENDFLIFKESASLMVDRIFSFEINVSVAIITFASEPKVLMSVLNDNSRDMTEVISSLENANYKDHENGTGTNTYAALNSVYLMMNNQMRLLGMETMAWQEIRHAIILLTDGKSNMGGSPKTAVDHIREILNINQKRNDYLDIYAIGVGKLDVDWRELNELGSKKDGERHAFILQDTKALHQVFEHMLDVSKLTDTICGVGNMSANASDQERTPWHVTIKPKSQETCRGALISDQWVLTAAHCFRDGNDHSLWRVNVGDPKSQWGKEFLIEKAVISPGFDVFAKKNQGILEFYGDDIALLKLAQKVKMSTHARPICLPCTMEANLALRRPQGSTCRDHENELLNKQSVPAHFVALNGSKLNINLKMGVEWTSCAEVVSQEKTMFPNLTDVREVVTDQFLCSGTQEDESPCKGESGGAVFLERRFRFFQVGLVSWGLYNPCLGSADKNSRKRAPRSKVPPPRDFHINLFRMQPWLRQHLGDVLNFLPL 752
               SCOP domains d2i6qa1 A:223-442 automated matches                                                                                                                                                                                         d2i6qa2 A:443-732 automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee.....eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee...eeeee...hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..hhhhhheeeeeeee.........hhhhhhhhhhhhhh..hhhhh.eeeeeeee.....hhhhhhhhh........eeee.hhhhhhhhhhhhee..................hhhhhh..eeeee......eeeee....eeeehhhhh....hhhhheeee........eee.eeeeee........hhhhh.........eeeee.................hhhhhhhh......hhhhhhhhhh...eeeeeee.....eeeeeee.hhhhhhhhhhhhhh........hhhhh....eeee........hhhhh..eeeeee..eeeeeeeeeee......-------.............eeeee...hhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------D-------------------------------------------------------------------------------------------------------------------------------------------------R--------------------------------------------------------------------L--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C------------------ SAPs(SNPs)
                PROSITE (1) -----------VWFA  PDB: A:234-432 UniProt: 254-452                                                                                                                                                                  -----------TRYPSIN_DOM  PDB: A:444-724 UniProt: 464-744                                                                                                                                                                                                                                             -------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSI--------------------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2i6q A 223 SKIQIQRSGHLNLYLLLDCSQSVSENDFLIFKESASLMVDRIFSFEINVSVAIITFASEPKVLMSVLNDNSRDMTEVISSLENANYKDHENGTGTNTYAALNSVYLMMNNQMRLLGMETMAWQEIRHAIILLTDGKSNMGGSPKTAVDHIREILNINQKRNDYLDIYAIGVGKLDVDWRELNELGSKKDGERHAFILQDTKALHQVFEHMLDVSKLTDTICGVGNMSANASDQERTPWHVTIKPKSQETCRGALISDQWVLTAAHCFRDGNDHSLWRVNVGDPKSQWGKEFLIEKAVISPGFDVFAKKNQGILEFYGDDIALLKLAQKVKMSTHARPICLPCTMEANLALRRPQGSTCRDHENELLNKQSVPAHFVALNGSKLNINLKMGVEWTSCAEVVSQEKTMFPNLTDVREVVTDQFLCSGTQEDESPCKGESGGAVFLERRFRFFQVGLVSWGLYNPCL-------RKRAPRSKVPPPRDFHINLFRMQPWLRQHLGDVLNFLPL 732
                                   232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682   |     - |     702       712       722       732
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         686     694                                      

Chain A from PDB  Type:PROTEIN  Length:503
 aligned with Q53HP3_HUMAN | Q53HP3 from UniProtKB/TrEMBL  Length:752

    Alignment length:510
                                   252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752
         Q53HP3_HUMAN   243 RKIQIQRSGHLNLYLLLDCSQSVSENDFLIFKESASLMVDRIFSFEINVSVAIITFASEPKVLMSVLNDNSRDMTEVISSLENANYKDHENGTGTNTYAALNSVYLMMNNQMRLLGMETMAWQEIRHAIILLTDGKSNMGGSPKTAVDHIREILNINQKRNDYLDIYAIGVGKLDVDWRELNELGSKKDGERHAFILQDTKALHQVFEHMLDVSKLTDTICGVGNMSANASDQERTPWHVTIKPKSQETCRGALISDQWVLTAAHCFRDGNDHSLWRVNVGDPKSQWGKEFLIEKAVISPGFDVFAKKNQGILEFYGDDIALLKLAQKVKMSTHARPICLPCTMEANLALRRPQGSTCRDHENELLNKQSVPAHFVALNGSKLNINLKMGVEWTSCAEVVSQEKTMFPNLTDVREVVTDQFLCSGTQEDESPCKGESGGAVFLERRFRFFQVGLVSWGLYNPCLGSADKNSRKRAPRSKVPPPRDFHINLFRMQPWLRQHLGDVLNFLPL 752
               SCOP domains d2i6qa1 A:223-442 automated matches                                                                                                                                                                                         d2i6qa2 A:443-732 automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee.....eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee...eeeee...hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..hhhhhheeeeeeee.........hhhhhhhhhhhhhh..hhhhh.eeeeeeee.....hhhhhhhhh........eeee.hhhhhhhhhhhhee..................hhhhhh..eeeee......eeeee....eeeehhhhh....hhhhheeee........eee.eeeeee........hhhhh.........eeeee.................hhhhhhhh......hhhhhhhhhh...eeeeeee.....eeeeeee.hhhhhhhhhhhhhh........hhhhh....eeee........hhhhh..eeeeee..eeeeeeeeeee......-------.............eeeee...hhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------D-------------------------------------------------------------------------------------------------------------------------------------------------R--------------------------------------------------------------------L--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2i6q A 223 SKIQIQRSGHLNLYLLLDCSQSVSENDFLIFKESASLMVDRIFSFEINVSVAIITFASEPKVLMSVLNDNSRDMTEVISSLENANYKDHENGTGTNTYAALNSVYLMMNNQMRLLGMETMAWQEIRHAIILLTDGKSNMGGSPKTAVDHIREILNINQKRNDYLDIYAIGVGKLDVDWRELNELGSKKDGERHAFILQDTKALHQVFEHMLDVSKLTDTICGVGNMSANASDQERTPWHVTIKPKSQETCRGALISDQWVLTAAHCFRDGNDHSLWRVNVGDPKSQWGKEFLIEKAVISPGFDVFAKKNQGILEFYGDDIALLKLAQKVKMSTHARPICLPCTMEANLALRRPQGSTCRDHENELLNKQSVPAHFVALNGSKLNINLKMGVEWTSCAEVVSQEKTMFPNLTDVREVVTDQFLCSGTQEDESPCKGESGGAVFLERRFRFFQVGLVSWGLYNPCL-------RKRAPRSKVPPPRDFHINLFRMQPWLRQHLGDVLNFLPL 732
                                   232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682   |     - |     702       712       722       732
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         686     694                                      

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2I6Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I6Q)

(-) Gene Ontology  (16, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CO2_HUMAN | P06681)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006956    complement activation    Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway.
    GO:0006958    complement activation, classical pathway    Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
    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:2000427    positive regulation of apoptotic cell clearance    Any process that activates or increases the frequency, rate or extent of apoptotic cell clearance.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0030449    regulation of complement activation    Any process that modulates the frequency, rate or extent of complement activation.
    GO:0007584    response to nutrient    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus.
cellular component
    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.

Chain A   (Q53HP3_HUMAN | Q53HP3)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006956    complement activation    Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CO2_HUMAN | P066812i6s 2odp 2odq 3erb
UniProtKB/TrEMBL
        Q53HP3_HUMAN | Q53HP32odp

(-) Related Entries Specified in the PDB File

2i6s