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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE FROM ERWINIA CAROTOVORA AT 1.9 RESOLUTION (CURRENT NAME, PECTOBACTERIUM CAROTOVORUM)
 
Authors :  C. Kim, N. -H. Xuong, S. Edwards, Madhusudan, M. -C. Yee, G. Spraggon, S. E. Mills
Date :  29 Nov 01  (Deposition) - 23 Oct 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Type 3 Prt Fold, Nucleotide Binding Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Kim, N. -H. Xuong, S. Edwards, Madhusudan, M. -C. Yee, G. Spraggon, S. E. Mills
The Crystal Structure Of Anthranilate Phosphoribosyltransferase From The Enterobacterium Pectobacterium Carotovorum
Febs Lett. V. 523 239 2002
PubMed-ID: 12123839  |  Reference-DOI: 10.1016/S0014-5793(02)02905-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.4.2.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC13
    Expression System Strain: JMB9 R-M+.TRPLDL02 LEU-THI-
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TRPD
    Organism Scientific: PECTOBACTERIUM CAROTOVORUM
    Organism Taxid: 554

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1KHD)

(-) Sites  (0, 0)

(no "Site" information available for 1KHD)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KHD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1KHD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KHD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KHD)

(-) Exons   (0, 0)

(no "Exon" information available for 1KHD)

(-) 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:324
 aligned with Q8VP84_PECCA | Q8VP84 from UniProtKB/TrEMBL  Length:345

    Alignment length:333
                                    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       311       321       331       341   
         Q8VP84_PECCA    12 THQPILEKLFKSQSMTQEESHQLFAAIVRGELEDSQLAAALISMKMRGERPEEIAGAASALLADAQPFPRPDYDFADIVGTGGDGTNSINISTASAFVAASCGAKVAKHGNRSVCQPLAGSCDLLQAFGIRLDMSAEDSRQALDDLNVCFLFAPQYHTGFRHAMPVRQQLKTRTIFNVLGPLINPARPPKALIGVYSPELVLPIAQALKVLGYKNAAVVHGGGMDEVAIHTPTQVAELNNGEIESYQLSPQDFGLQSYSLNALQGGTPEENRDILARLLQGKGDAAHARQVAANVALLLKLFGQDNLRHNAQLALETIRSGTAFERVTALAAR 344
               SCOP domains d1khda1 A:12-80 Anthranilate phosphoribosyltransferase (TrpD)        d1khda2 A:81-344 Anthranilate phosphoribosy         ltransferase (TrpD)                                                                                                                                                                                                  SCOP domains
               CATH domains 1khdA01 A:12-78,A:164-196                                          -----1khdA02 A:84-163,A:197-343                                                      1khdA01 A:12-78,A:164-196        1khdA02 A:84-163,A:197-343 Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2                                                                  - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...........eeeee..........hhhhhhhhhhhh...eeeee..---------hhhhhhh......hhhhhhhhhhhhheeeeehhhhhhhhhhhhhhhhhhh...hhhhhhhhh......eeeee..hhhhhhhhhhhhhhh...eeeeeee...........eeeeeee..eeeeeeehhhhhh....hhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1khd A  12 THQPILEKLFKSQSMTQEESHQLFAAIVRGELEDSQLAAALISMKMRGERPEEIAGAASALLADAQPFPRPDYDFADIVGTGGDGTNSINISTASAFVAASCGAKVAKHGNR---------CDLLQAFGIRLDMSAEDSRQALDDLNVCFLFAPQYHTGFRHAMPVRQQLKTRTIFNVLGPLINPARPPKALIGVYSPELVLPIAQALKVLGYKNAAVVHGGGMDEVAIHTPTQVAELNNGEIESYQLSPQDFGLQSYSLNALQGGTPEENRDILARLLQGKGDAAHARQVAANVALLLKLFGQDNLRHNAQLALETIRSGTAFERVTALAAR 344
                                    21        31        41        51        61        71        81        91       101       111       121 |       - |     141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341   
                                                                                                                                         123       133                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:328
 aligned with Q8VP84_PECCA | Q8VP84 from UniProtKB/TrEMBL  Length:345

    Alignment length:333
                                    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       311       321       331       341   
         Q8VP84_PECCA    12 THQPILEKLFKSQSMTQEESHQLFAAIVRGELEDSQLAAALISMKMRGERPEEIAGAASALLADAQPFPRPDYDFADIVGTGGDGTNSINISTASAFVAASCGAKVAKHGNRSVCQPLAGSCDLLQAFGIRLDMSAEDSRQALDDLNVCFLFAPQYHTGFRHAMPVRQQLKTRTIFNVLGPLINPARPPKALIGVYSPELVLPIAQALKVLGYKNAAVVHGGGMDEVAIHTPTQVAELNNGEIESYQLSPQDFGLQSYSLNALQGGTPEENRDILARLLQGKGDAAHARQVAANVALLLKLFGQDNLRHNAQLALETIRSGTAFERVTALAAR 344
               SCOP domains d1khdb1 B:12-80 Anthranilate phosphoribosyltransferase (TrpD)        d1khdb2 B:81-344 Anthranilate phosphoribosy     ltransferase (TrpD)                                                                                                                                                                                                      SCOP domains
               CATH domains 1khdB01 B:12-78,B:164-196                                          -----1khdB02 B:84-163,B:197-343                                                      1khdB01 B:12-78,B:164-196        1khdB02 B:84-163,B:197-343 Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2                                                                  - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...........eeeee..........hhhhhhhhhhhhh..eeeee..-----..hhhhhhhhh......hhhhhhhhhhhhheeeeehhhhh.hhhhhhhhhhhhh...hhhhhhhhh......eeeee..hhhhhhhhhhhhhhh...eeeeeee...........eeeeeee..eeeeeeehhhhhh....hhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1khd B  12 THQPILEKLFKSQSMTQEESHQLFAAIVRGELEDSQLAAALISMKMRGERPEEIAGAASALLADAQPFPRPDYDFADIVGTGGDGTNSINISTASAFVAASCGAKVAKHGNR-----LAGSCDLLQAFGIRLDMSAEDSRQALDDLNVCFLFAPQYHTGFRHAMPVRQQLKTRTIFNVLGPLINPARPPKALIGVYSPELVLPIAQALKVLGYKNAAVVHGGGMDEVAIHTPTQVAELNNGEIESYQLSPQDFGLQSYSLNALQGGTPEENRDILARLLQGKGDAAHARQVAANVALLLKLFGQDNLRHNAQLALETIRSGTAFERVTALAAR 344
                                    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       311       321       331       341   
                                                                                                                                         123   129                                                                                                                                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:320
 aligned with Q8VP84_PECCA | Q8VP84 from UniProtKB/TrEMBL  Length:345

    Alignment length:334
                                    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       311       321       331       341    
         Q8VP84_PECCA    12 THQPILEKLFKSQSMTQEESHQLFAAIVRGELEDSQLAAALISMKMRGERPEEIAGAASALLADAQPFPRPDYDFADIVGTGGDGTNSINISTASAFVAASCGAKVAKHGNRSVCQPLAGSCDLLQAFGIRLDMSAEDSRQALDDLNVCFLFAPQYHTGFRHAMPVRQQLKTRTIFNVLGPLINPARPPKALIGVYSPELVLPIAQALKVLGYKNAAVVHGGGMDEVAIHTPTQVAELNNGEIESYQLSPQDFGLQSYSLNALQGGTPEENRDILARLLQGKGDAAHARQVAANVALLLKLFGQDNLRHNAQLALETIRSGTAFERVTALAARG 345
               SCOP domains d1khdc1 C:12-80 Anthranilate phosphoribosyltransferase (TrpD)        d1khdc2 C:81-     345 Anthranilate phospho         ribosyltransferase (TrpD)                                                                                                                                                                                              SCOP domains
               CATH domains 1khdC01 C:12-78,C:164-196                                          -----1khdC02 C:     84-163,C:197-343                                                 1khdC01 C:12-78,C:164-196        1khdC02 C:84-163,C:197-343 Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2                                                                  -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..........eeeee..-----..hhhhhhhhhhhh....eeeee.---------hhhhhhhh......hhhhhhhhhhhhheeeeehhhhhhhhhhhhhhhhhhh...hhhhhhhhh......eeeee..hhhhhhhhhhhhhhh...eeeeeee...........eeeeeee..eeeeeeehhhhhh....hhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1khd C  12 THQPILEKLFKSQSMTQEESHQLFAAIVRGELEDSQLAAALISMKMRGERPEEIAGAASALLADAQPFPRPDYDFADIVGTG-----SINISTASAFVAASCGAKVAKHGN---------SCDLLQAFGIRLDMSAEDSRQALDDLNVCFLFAPQYHTGFRHAMPVRQQLKTRTIFNVLGPLINPARPPKALIGVYSPELVLPIAQALKVLGYKNAAVVHGGGMDEVAIHTPTQVAELNNGEIESYQLSPQDFGLQSYSLNALQGGTPEENRDILARLLQGKGDAAHARQVAANVALLLKLFGQDNLRHNAQLALETIRSGTAFERVTALAARG 345
                                    21        31        41        51        61        71        81        91 |     101       111       121|        -|      141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341    
                                                                                                            93    99                    122       132                                                                                                                                                                                                                     


Chain D from PDB  Type:PROTEIN  Length:329
 aligned with Q8VP84_PECCA | Q8VP84 from UniProtKB/TrEMBL  Length:345

    Alignment length:333
                                    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       311       321       331       341   
         Q8VP84_PECCA    12 THQPILEKLFKSQSMTQEESHQLFAAIVRGELEDSQLAAALISMKMRGERPEEIAGAASALLADAQPFPRPDYDFADIVGTGGDGTNSINISTASAFVAASCGAKVAKHGNRSVCQPLAGSCDLLQAFGIRLDMSAEDSRQALDDLNVCFLFAPQYHTGFRHAMPVRQQLKTRTIFNVLGPLINPARPPKALIGVYSPELVLPIAQALKVLGYKNAAVVHGGGMDEVAIHTPTQVAELNNGEIESYQLSPQDFGLQSYSLNALQGGTPEENRDILARLLQGKGDAAHARQVAANVALLLKLFGQDNLRHNAQLALETIRSGTAFERVTALAAR 344
               SCOP domains d1khdd1 D:12-80 Anthranilate phosphoribosyltransferase (TrpD)        d1khdd2 D:81-344   Anthranilate phosphoribos  yltransferase (TrpD)                                                                                                                                                                                                       SCOP domains
               CATH domains 1khdD01 D:12-78,D:164-196                                          -----1khdD02 D:84-  163,D:197-343                                                    1khdD01 D:12-78,D:164-196        1khdD02 D:84-163,D:197-343 Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2                                                                  - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhh...........................eeeee.....--..hhhhhhhhhhhhh...eeeee...--....hhhhhhhhh......hhhhhhhhhhhhheeeeehhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......eeeee..hhhhhhhhhhhhhhhh..eeeeeee...........eeeeeee..eeeeeeehhhhhh....hhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1khd D  12 THQPILEKLFKSQSMTQEESHQLFAAIVRGELEDSQLAAALISMKMRGERPEEIAGAASALLADAQPFPRPDYDFADIVGTGGDG--SINISTASAFVAASCGAKVAKHGNRS--QPLAGSCDLLQAFGIRLDMSAEDSRQALDDLNVCFLFAPQYHTGFRHAMPVRQQLKTRTIFNVLGPLINPARPPKALIGVYSPELVLPIAQALKVLGYKNAAVVHGGGMDEVAIHTPTQVAELNNGEIESYQLSPQDFGLQSYSLNALQGGTPEENRDILARLLQGKGDAAHARQVAANVALLLKLFGQDNLRHNAQLALETIRSGTAFERVTALAAR 344
                                    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       311       321       331       341   
                                                                                                               96 99                      124  |                                                                                                                                                                                                                         
                                                                                                                                             127
   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, 8)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1KHD)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8VP84_PECCA | Q8VP84)
molecular function
    GO:0004048    anthranilate phosphoribosyltransferase activity    Catalysis of the reaction: N-(5-phospho-beta-D-ribosyl)anthranilate + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + anthranilate.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0009073    aromatic amino acid family biosynthetic process    The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    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.
    GO:0000162    tryptophan biosynthetic process    The chemical reactions and pathways resulting in the formation of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid; tryptophan is synthesized from chorismate via anthranilate.

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  1khd
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 Related Entries

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

UniProtKB/TrEMBL
        Q8VP84_PECCA | Q8VP84: 1kgz

(-) Related Entries Specified in the PDB File

1kgz 1KGZ IS THE CRYSTAL STRUCTURE ANALYSIS OF THE ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE FROM ERWINIA CAROTOVORA (CURRENT NAME, PECTOBACTERIUM CAROTOVORUM).