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(-) Description

Title :  CRYSTAL STRUCTURE OF THE YERSINIA PESTIS DIHYDROPTEROATE SYNTHETASE WITH SUBSTRATE TRANSITION STATE COMPLEX.
 
Authors :  Y. Wu
Date :  26 Sep 11  (Deposition) - 14 Mar 12  (Release) - 14 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dihydropteroate Synthase, Transition State Complex, Paba, Tim Barrel, Transferase-Transferase Substrate Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. K. Yun, Y. Wu, Z. Li, Y. Zhao, M. B. Waddell, A. M. Ferreira, R. E. Lee, D. Bashford, S. W. White
Catalysis And Sulfa Drug Resistance In Dihydropteroate Synthase.
Science V. 335 1110 2012
PubMed-ID: 22383850  |  Reference-DOI: 10.1126/SCIENCE.1214641

(-) Compounds

Molecule 1 - 7,8-DIHYDROPTEROATE SYNTHASE
    Chains: A, B
    EC Number: 2.5.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DHPS, FOLP, Y0683, YPO3501, YP_0582
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 632
    Strain: KIM D27
    Synonym: DIHYDROPTEROATE SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2PAB2Ligand/Ion4-AMINOBENZOIC ACID
3POP2Ligand/IonPYROPHOSPHATE 2-
4XHP2Ligand/Ion2-AMINO-6-METHYLIDENE-6,7-DIHYDROPTERIDIN-4(3H)-ONE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:96 , ASN A:115 , ILE A:117 , ASP A:185 , PHE A:190 , LEU A:215 , GLY A:217 , LYS A:221 , ARG A:255 , POP A:279 , PAB A:280 , HOH A:352BINDING SITE FOR RESIDUE XHP A 278
2AC2SOFTWAREASN A:22 , SER A:27 , PHE A:28 , SER A:61 , THR A:62 , ARG A:63 , ARG A:255 , HIS A:257 , XHP A:278 , PAB A:280 , MG A:281 , HOH A:303 , HOH A:307 , HOH A:322BINDING SITE FOR RESIDUE POP A 279
3AC3SOFTWAREPHE A:28 , THR A:62 , ARG A:63 , PHE A:190 , LYS A:221 , SER A:222 , XHP A:278 , POP A:279 , HOH A:289 , HOH A:290 , HOH A:320BINDING SITE FOR RESIDUE PAB A 280
4AC4SOFTWAREASN A:22 , SER A:27 , POP A:279 , HOH A:305 , HOH A:306 , HOH A:307BINDING SITE FOR RESIDUE MG A 281
5AC5SOFTWAREASP B:96 , ASN B:115 , ILE B:117 , MET B:139 , ASP B:185 , PHE B:190 , LEU B:215 , GLY B:217 , LYS B:221 , ARG B:255 , POP B:279 , PAB B:280 , HOH B:283 , HOH B:295BINDING SITE FOR RESIDUE XHP B 278
6AC6SOFTWAREASN B:22 , SER B:27 , PHE B:28 , SER B:61 , THR B:62 , ARG B:63 , ARG B:255 , HIS B:257 , XHP B:278 , PAB B:280 , MG B:281 , HOH B:283 , HOH B:287 , HOH B:303BINDING SITE FOR RESIDUE POP B 279
7AC7SOFTWAREPHE B:28 , THR B:62 , ARG B:63 , GLY B:189 , PHE B:190 , LYS B:221 , SER B:222 , XHP B:278 , POP B:279 , HOH B:292 , HOH B:293BINDING SITE FOR RESIDUE PAB B 280
8AC8SOFTWAREASN B:22 , POP B:279 , HOH B:282 , HOH B:283 , HOH B:284BINDING SITE FOR RESIDUE MG B 281

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3TYZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TYZ)

(-) 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:275
 aligned with Q7CKJ1_YERPE | Q7CKJ1 from UniProtKB/TrEMBL  Length:277

    Alignment length:275
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270     
         Q7CKJ1_YERPE     1 MHLTARGLTLDLSRPQVMGILNVTPDSFSDGGCHNNLDQALQHAQRMLSAGATLIDIGGESTRPGAAEVSEQEELDRVVPVVEALAQRFDVWLSVDTSKAAVITESAHAGAHLINDIRSLQEPGALEAAAKTGLPVCLMHMQGQPKNMQHSPYYDDLMTDINRFFQHHIERCVAAGIAKNKLLLDPGFGFGKNLAHNYQLLAHLSELHHFELPLLVGMSRKSMVGQLLNVPPQQRVIGSVACAVIAAMQGAQIIRVHDVKETVEAMCIVEATRSA 275
               SCOP domains d3tyza_ A: automated matches                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeee....eeeeeee.............hhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eeee.......hhhhhhhhhh..eeee................hhhhhhhhhhhhhhhhhhhh..hhh.eeee.......hhhhhhhhhhhhhhhhhhh...ee....hhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tyz A   1 MHLTARGLTLDLSRPQVMGILNVTPDSFSDGGCHNNLDQALQHAQRMLSAGATLIDIGGESTRPGAAEVSEQEELDRVVPVVEALAQRFDVWLSVDTSKAAVITESAHAGAHLINDIRSLQEPGALEAAAKTGLPVCLMHMQGQPKNMQHSPYYDDLMTDINRFFQHHIERCVAAGIAKNKLLLDPGFGFGKNLAHNYQLLAHLSELHHFELPLLVGMSRKSMVGQLLNVPPQQRVIGSVACAVIAAMQGAQIIRVHDVKETVEAMCIVEATRSA 275
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270     


Chain B from PDB  Type:PROTEIN  Length:276
 aligned with Q7CKJ1_YERPE | Q7CKJ1 from UniProtKB/TrEMBL  Length:277

    Alignment length:276
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270      
         Q7CKJ1_YERPE     1 MHLTARGLTLDLSRPQVMGILNVTPDSFSDGGCHNNLDQALQHAQRMLSAGATLIDIGGESTRPGAAEVSEQEELDRVVPVVEALAQRFDVWLSVDTSKAAVITESAHAGAHLINDIRSLQEPGALEAAAKTGLPVCLMHMQGQPKNMQHSPYYDDLMTDINRFFQHHIERCVAAGIAKNKLLLDPGFGFGKNLAHNYQLLAHLSELHHFELPLLVGMSRKSMVGQLLNVPPQQRVIGSVACAVIAAMQGAQIIRVHDVKETVEAMCIVEATRSAK 276
               SCOP domains d3tyzb_ B: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eeee....eeeeeee.............hhhhhhhhhhhhhhh...eeeee...........hhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhh...eeee.......hhhhhhhhhh..eeee................hhhhhhhhhhhhhhhhhhhh..hhh.eeee.......hhhhhhhhhhhhhhhhhhh...ee....hhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tyz B   1 MHLTARGLTLDLSRPQVMGILNVTPDSFSDGGCHNNLDQALQHAQRMLSAGATLIDIGGESTRPGAAEVSEQEELDRVVPVVEALAQRFDVWLSVDTSKAAVITESAHAGAHLINDIRSLQEPGALEAAAKTGLPVCLMHMQGQPKNMQHSPYYDDLMTDINRFFQHHIERCVAAGIAKNKLLLDPGFGFGKNLAHNYQLLAHLSELHHFELPLLVGMSRKSMVGQLLNVPPQQRVIGSVACAVIAAMQGAQIIRVHDVKETVEAMCIVEATRSAK 276
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q7CKJ1_YERPE | Q7CKJ1)
molecular function
    GO:0004156    dihydropteroate synthase activity    Catalysis of the reaction: 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine diphosphate + 4-aminobenzoate = diphosphate + dihydropteroate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0044237    cellular metabolic process    The chemical reactions and pathways by which individual cells transform chemical substances.
    GO:0046656    folic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of folic acid, pteroylglutamic acid.
    GO:0009396    folic acid-containing compound biosynthetic process    The chemical reactions and pathways resulting in the formation of folic acid and its derivatives.
    GO:0042558    pteridine-containing compound metabolic process    The chemical reactions and pathways involving any compound containing pteridine (pyrazino(2,3-dipyrimidine)), e.g. pteroic acid, xanthopterin and folic acid.
    GO:0046654    tetrahydrofolate biosynthetic process    The chemical reactions and pathways resulting in the formation of tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.

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 Related Entries

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

UniProtKB/TrEMBL
        Q7CKJ1_YERPE | Q7CKJ1: 3tyu 3tzf 3tzn 5jq9

(-) Related Entries Specified in the PDB File

3tyu 3tzf 3tzn