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(-) Description

Title :  CRYSTAL STRUCTURE OF YAGE, A PROPHAGE PROTEIN BELONGING TO THE DIHYDRODIPICOLINIC ACID SYNTHASE FAMILY FROM E. COLI K12 IN COMPLEX WITH PYRUVATE
 
Authors :  V. Bhaskar, P. M. Kumar, S. Manicka, S. Krishnaswamy
Date :  19 May 10  (Deposition) - 13 Apr 11  (Release) - 13 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tim Barrel, Protein-Ligand Complex, Aldolase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Bhaskar, M. Kumar, S. Manicka, S. Tripathi, A. Venkatraman, S. Krishnaswamy
Identification Of Biochemical And Putative Biological Role Of A Xenolog From Escherichia Coli Using Structural Analysis.
Proteins V. 79 1132 2011
PubMed-ID: 21294156  |  Reference-DOI: 10.1002/PROT.22949

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN YAGE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 12-309
    Gene: B0268, JW0261, YAGE
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: A CP4-6 PROPHAGE PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2MCL4Mod. Amino AcidNZ-(1-CARBOXYETHYL)-LYSINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:54 , PHE A:60 , ARG A:68 , GLY A:88 , THR A:89 , GLY A:90 , VAL A:113 , VAL A:114 , ILE A:115 , TYR A:145BINDING SITE FOR RESIDUE EDO A 1
2AC2SOFTWARELEU B:54 , PHE B:60 , ARG B:68 , GLY B:88 , THR B:89 , GLY B:90 , VAL B:113 , VAL B:114 , ILE B:115BINDING SITE FOR RESIDUE EDO B 2
3AC3SOFTWARELEU C:54 , PHE C:60 , ARG C:68 , GLY C:88 , THR C:89 , GLY C:90 , VAL C:113 , VAL C:114 , ILE C:115 , TYR C:145BINDING SITE FOR RESIDUE EDO C 3
4AC4SOFTWARELEU D:54 , PHE D:60 , ARG D:68 , GLY D:88 , GLY D:90 , VAL D:113 , VAL D:114 , ILE D:115 , TYR D:145BINDING SITE FOR RESIDUE EDO D 4

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N2X)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Thr A:263 -Pro A:264
2Pro A:286 -Pro A:287
3Thr B:263 -Pro B:264
4Pro B:286 -Pro B:287
5Thr C:263 -Pro C:264
6Pro C:286 -Pro C:287
7Thr D:263 -Pro D:264
8Pro D:286 -Pro D:287

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N2X)

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHDPS_1PS00665 Dihydrodipicolinate synthase signature 1.YAGE_ECOLI43-60
 
 
 		  4A:50-67
B:50-67
C:50-67
D:50-67
2DHDPS_2PS00666 Dihydrodipicolinate synthase signature 2.YAGE_ECOLI138-169
 
 
 		  4A:145-176
B:145-176
C:145-176
D:145-176

(-) Exons   (0, 0)

(no "Exon" information available for 3N2X)

(-) 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:298
 aligned with YAGE_ECOLI | P75682 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:298
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294        
           YAGE_ECOLI     5 ALFTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIARFAIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQVADSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMIHTVKGAHPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLLQIPQMYQLDTPFVNVIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLKTLLQQLKLC 302
               SCOP domains d3n2xa_ A: automated matches                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..ee..........hhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhh...ee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh...............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------DHDPS_1           -----------------------------------------------------------------------------DHDPS_2  PDB: A:145-176         ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n2x A  12 ALFTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIARFAIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQVADSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIkDTIDSVAHLRSMIHTVKGAHPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLLQIPQMYQLDTPFVNVIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLKTLLQQLKLC 309
                                    21        31        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        
                                                                                                                                                                                            174-MCL                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:298
 aligned with YAGE_ECOLI | P75682 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:298
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294        
           YAGE_ECOLI     5 ALFTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIARFAIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQVADSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMIHTVKGAHPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLLQIPQMYQLDTPFVNVIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLKTLLQQLKLC 302
               SCOP domains d3n2xb_ B: automated matches                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..............hhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhh...ee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------DHDPS_1           -----------------------------------------------------------------------------DHDPS_2  PDB: B:145-176         ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n2x B  12 ALFTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIARFAIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQVADSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIkDTIDSVAHLRSMIHTVKGAHPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLLQIPQMYQLDTPFVNVIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLKTLLQQLKLC 309
                                    21        31        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        
                                                                                                                                                                                            174-MCL                                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:298
 aligned with YAGE_ECOLI | P75682 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:298
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294        
           YAGE_ECOLI     5 ALFTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIARFAIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQVADSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMIHTVKGAHPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLLQIPQMYQLDTPFVNVIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLKTLLQQLKLC 302
               SCOP domains d3n2xc_ C: automated matches                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..............hhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhh...ee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------DHDPS_1           -----------------------------------------------------------------------------DHDPS_2  PDB: C:145-176         ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n2x C  12 ALFTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIARFAIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQVADSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIkDTIDSVAHLRSMIHTVKGAHPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLLQIPQMYQLDTPFVNVIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLKTLLQQLKLC 309
                                    21        31        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        
                                                                                                                                                                                            174-MCL                                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:298
 aligned with YAGE_ECOLI | P75682 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:298
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294        
           YAGE_ECOLI     5 ALFTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIARFAIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQVADSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMIHTVKGAHPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLLQIPQMYQLDTPFVNVIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLKTLLQQLKLC 302
               SCOP domains d3n2xd_ D: automated matches                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------DHDPS-3n2xD01 D:20-309                                                                                                                                                                                                                                                                             Pfam domains (1)
           Pfam domains (2) --------DHDPS-3n2xD02 D:20-309                                                                                                                                                                                                                                                                             Pfam domains (2)
           Pfam domains (3) --------DHDPS-3n2xD03 D:20-309                                                                                                                                                                                                                                                                             Pfam domains (3)
           Pfam domains (4) --------DHDPS-3n2xD04 D:20-309                                                                                                                                                                                                                                                                             Pfam domains (4)
         Sec.struct. author ....ee..............hhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhh..ee.hhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------DHDPS_1           -----------------------------------------------------------------------------DHDPS_2  PDB: D:145-176         ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n2x D  12 ALFTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIARFAIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQVADSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIkDTIDSVAHLRSMIHTVKGAHPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLLQIPQMYQLDTPFVNVIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLKTLLQQLKLC 309
                                    21        31        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        
                                                                                                                                                                                            174-MCL
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N2X)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (YAGE_ECOLI | P75682)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0046176    aldonic acid catabolic process    The chemical reactions and pathways resulting in the breakdown of aldonic acid, a monocarboxylic acid with a chain of three or more carbon atoms, derived from an aldose by oxidation of the aldehydic group.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  YAGE_ECOLI | P75682
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 Related Entries

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

UniProtKB/Swiss-Prot
        YAGE_ECOLI | P75682: 2v8z 2v9d 3nev 4oe7 4onv 4ptn 4u4m

(-) Related Entries Specified in the PDB File

2v8z CRYSTAL STRUCTURE OF YAGE, A PUTATIVE DHDPS-LIKE PROTEIN FROM ESCHERICHIA COLI K12.
2v9d CRYSTAL STRUCTURE OF YAGE, A PROPHAGE PROTEIN BELONGING TO THE DIHYDRODIPICOLINIC ACID SYNTHASE FAMILY FROM E. COLI K12