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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LAMININ-BINDING PROTEIN LBP OF STREPTOCOCCUS PYOGENES
 
Authors :  C. Linke, T. T. Caradoc-Davies, P. G. Young, T. Proft, E. N. Baker
Date :  04 Mar 09  (Deposition) - 04 Aug 09  (Release) - 08 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Zinc-Binding Receptor, Metal-Binding, Helical Backbone, Alpha/Beta Domains, Laminin-Binding Protein, Lbp, Transport, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Linke, T. T. Caradoc-Davies, P. G. Young, T. Proft, E. N. Baker
The Laminin-Binding Protein Lbp From Streptococcus Pyogenes Is A Zinc Receptor
J. Bacteriol. V. 191 5814 2009
PubMed-ID: 19617361  |  Reference-DOI: 10.1128/JB.00485-09
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LAMININ-BINDING PROTEIN OF GROUP A STREPTOCOCCI
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST17
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 24-306
    Gene: LMB, LMB/SPY_2007
    Organism Scientific: STREPTOCOCCUS PYOGENES
    Organism Taxid: 1314
    Strain: SEROTYPE M1 SF370
    Synonym: LBP

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:66 , HIS A:142 , HIS A:206 , ILE A:226 , GLU A:281BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWAREHIS B:66 , HIS B:142 , HIS B:206 , ILE B:226 , GLU B:281BINDING SITE FOR RESIDUE ZN B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GI1)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:121 -Lys A:122
2Glu B:229 -Gln B:230

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GI1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GI1)

(-) Exons   (0, 0)

(no "Exon" information available for 3GI1)

(-) 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:254
 aligned with Q7DII5_STRPY | Q7DII5 from UniProtKB/TrEMBL  Length:306

    Alignment length:277
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       
         Q7DII5_STRPY    30 TQGMSVVTSFYPMYAMTKEVSGDLNDVRMIQSGAGIHSFEPSVNDVAAIYDADLFVYHSHTLEAWARDLDPNLKKSKVDVFEASKPLTLDRVKGLEDMEVTQGIDPATLYDPHTWTDPVLAGEEAVNIAKELGRLDPKHKDSYTKNAKAFKKEAEQLTEEYTQKFKKVRSKTFVTQHTAFSYLAKRFGLKQLGISGISPEQEPSPRQLKEIQDFVKEYNVKTIFAEDNVNPKIAHAIAKSTGAKVKTLSPLEAAPSGNKTYLENLRANLEVLYQQLK 306
               SCOP domains d3gi1a_ A: automated matches                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3gi1A01 A:30-197 Nitrogenase m     olybdenum iron protein domain                                                                                                        3gi1A02 A:198-306 Nitrogenase m   olybdenum iron protein domain                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.hhhhhhhhhhhhh...eeee.-----......hhhhhhhhhh..eeee.....hhhhh...........eeee...........---------------....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhh..eeeeee....---.hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhh...eeee............hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gi1 A  30 TQGMSVVTSFYPMYAMTKEVSGDLNDVRMI-----IHSFEPSVNDVAAIYDADLFVYHSHTLEAWARDLDPNLKKSKVDVFEASKPLTLDRVK---------------LYDPHTWTDPVLAGEEAVNIAKELGRLDPKHKDSYTKNAKAFKKEAEQLTEEYTQKFKKVRSKTFVTQHTAFSYLAKRFGLKQLGISGISP---PSPRQLKEIQDFVKEYNVKTIFAEDNVNPKIAHAIAKSTGAKVKTLSPLEAAPSGNKTYLENLRANLEVLYQQLK 306
                                    39        49        59     |  69        79        89        99       109       119  |      -       139       149       159       169       179       189       199       209       219        |-  |    239       249       259       269       279       289       299       
                                                        59    65                                                      122             138                                                                                       228 232                                                                          


Chain A from PDB  Type:PROTEIN  Length:254
 aligned with Q99XV3_STRP1 | Q99XV3 from UniProtKB/TrEMBL  Length:306

    Alignment length:277
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       
         Q99XV3_STRP1    30 TQGMSVVTSFYPMYAMTKEVSGDLNDVRMIQSGAGIHSFEPSVNDVAAIYDADLFVYHSHTLEAWARDLDPNLKKSKVDVFEASKPLTLDRVKGLEDMEVTQGIDPATLYDPHTWTDPVLAGEEAVNIAKELGRLDPKHKDSYTKNAKAFKKEAEQLTEEYTQKFKKVRSKTFVTQHTAFSYLAKRFGLKQLGISGISPEQEPSPRQLKEIQDFVKEYNVKTIFAEDNVNPKIAHAIAKSTGAKVKTLSPLEAAPSGNKTYLENLRANLEVLYQQLK 306
               SCOP domains d3gi1a_ A: automated matches                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3gi1A01 A:30-197 Nitrogenase m     olybdenum iron protein domain                                                                                                        3gi1A02 A:198-306 Nitrogenase m   olybdenum iron protein domain                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.hhhhhhhhhhhhh...eeee.-----......hhhhhhhhhh..eeee.....hhhhh...........eeee...........---------------....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhh..eeeeee....---.hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhh...eeee............hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gi1 A  30 TQGMSVVTSFYPMYAMTKEVSGDLNDVRMI-----IHSFEPSVNDVAAIYDADLFVYHSHTLEAWARDLDPNLKKSKVDVFEASKPLTLDRVK---------------LYDPHTWTDPVLAGEEAVNIAKELGRLDPKHKDSYTKNAKAFKKEAEQLTEEYTQKFKKVRSKTFVTQHTAFSYLAKRFGLKQLGISGISP---PSPRQLKEIQDFVKEYNVKTIFAEDNVNPKIAHAIAKSTGAKVKTLSPLEAAPSGNKTYLENLRANLEVLYQQLK 306
                                    39        49        59     |  69        79        89        99       109       119  |      -       139       149       159       169       179       189       199       209       219        |-  |    239       249       259       269       279       289       299       
                                                        59    65                                                      122             138                                                                                       228 232                                                                          


Chain B from PDB  Type:PROTEIN  Length:254
 aligned with Q7DII5_STRPY | Q7DII5 from UniProtKB/TrEMBL  Length:306

    Alignment length:275
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301     
         Q7DII5_STRPY    32 GMSVVTSFYPMYAMTKEVSGDLNDVRMIQSGAGIHSFEPSVNDVAAIYDADLFVYHSHTLEAWARDLDPNLKKSKVDVFEASKPLTLDRVKGLEDMEVTQGIDPATLYDPHTWTDPVLAGEEAVNIAKELGRLDPKHKDSYTKNAKAFKKEAEQLTEEYTQKFKKVRSKTFVTQHTAFSYLAKRFGLKQLGISGISPEQEPSPRQLKEIQDFVKEYNVKTIFAEDNVNPKIAHAIAKSTGAKVKTLSPLEAAPSGNKTYLENLRANLEVLYQQLK 306
               SCOP domains d3gi1b_ B: automated matches                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 3gi1B01 B:32-197 Nitrogenase      molybdenum iron protein domain                                                                                                      3gi1B02 B:198-306 Nitrogenase molybdenum iron protein domain                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhhhhhhhhhh...eeee.-----......hhhhhhhhhh..eeee.....hhhhh...........eeee..........----------------....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee..hhhhhhhh..eeeeee........hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh.eeee............hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gi1 B  32 GMSVVTSFYPMYAMTKEVSGDLNDVRMI-----IHSFEPSVNDVAAIYDADLFVYHSHTLEAWARDLDPNLKKSKVDVFEASKPLTLDRV----------------LYDPHTWTDPVLAGEEAVNIAKELGRLDPKHKDSYTKNAKAFKKEAEQLTEEYTQKFKKVRSKTFVTQHTAFSYLAKRFGLKQLGISGISPEQEPSPRQLKEIQDFVKEYNVKTIFAEDNVNPKIAHAIAKSTGAKVKTLSPLEAAPSGNKTYLENLRANLEVLYQQLK 306
                                    41        51       | -   |    71        81        91       101       111       121         -      |141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301     
                                                      59    65                                                     121              138                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:254
 aligned with Q99XV3_STRP1 | Q99XV3 from UniProtKB/TrEMBL  Length:306

    Alignment length:275
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301     
         Q99XV3_STRP1    32 GMSVVTSFYPMYAMTKEVSGDLNDVRMIQSGAGIHSFEPSVNDVAAIYDADLFVYHSHTLEAWARDLDPNLKKSKVDVFEASKPLTLDRVKGLEDMEVTQGIDPATLYDPHTWTDPVLAGEEAVNIAKELGRLDPKHKDSYTKNAKAFKKEAEQLTEEYTQKFKKVRSKTFVTQHTAFSYLAKRFGLKQLGISGISPEQEPSPRQLKEIQDFVKEYNVKTIFAEDNVNPKIAHAIAKSTGAKVKTLSPLEAAPSGNKTYLENLRANLEVLYQQLK 306
               SCOP domains d3gi1b_ B: automated matches                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 3gi1B01 B:32-197 Nitrogenase      molybdenum iron protein domain                                                                                                      3gi1B02 B:198-306 Nitrogenase molybdenum iron protein domain                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhhhhhhhhhh...eeee.-----......hhhhhhhhhh..eeee.....hhhhh...........eeee..........----------------....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee..hhhhhhhh..eeeeee........hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh.eeee............hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gi1 B  32 GMSVVTSFYPMYAMTKEVSGDLNDVRMI-----IHSFEPSVNDVAAIYDADLFVYHSHTLEAWARDLDPNLKKSKVDVFEASKPLTLDRV----------------LYDPHTWTDPVLAGEEAVNIAKELGRLDPKHKDSYTKNAKAFKKEAEQLTEEYTQKFKKVRSKTFVTQHTAFSYLAKRFGLKQLGISGISPEQEPSPRQLKEIQDFVKEYNVKTIFAEDNVNPKIAHAIAKSTGAKVKTLSPLEAAPSGNKTYLENLRANLEVLYQQLK 306
                                    41        51       | -   |    71        81        91       101       111       121         -      |141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301     
                                                      59    65                                                     121              138
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GI1)

(-) Gene Ontology  (4, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q7DII5_STRPY | Q7DII5)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0030001    metal ion transport    The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

Chain A,B   (Q99XV3_STRP1 | Q99XV3)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0030001    metal ion transport    The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

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