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(-) Description

Title :  STRUCTURAL GENOMICS, A PROTEIN FROM SALMONELLA TYPHIMURIUM SIMILAR TO E. COLI ACYL CARRIER PROTEIN PHOSPHODIESTERASE
 
Authors :  R. Zhang, R. Wu, F. Collart, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  03 May 04  (Deposition) - 03 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Acyl Carrier Protein Phosphodiesterase, Fmn, Alpha/Beta/Alpha Sandwich, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Zhang, R. Wu, F. Collart, A. Joachimiak
1. 4 A Crystal Structure Of A Protein From Salmonella Typhimurium Similar To E. Coli Acyl Carrier Protein Phosphodiesterase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ACYL CARRIER PROTEIN PHOSPHODIESTERASE
    Atcc: 700720
    Chains: A, B
    EC Number: 3.1.4.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PDM68
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: ACPD, STM1642, STY1427, T1545
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602
    Synonym: ACP PHOSPHODIESTERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:10 , LEU A:12 , SER A:16 , GLN A:17 , SER A:18 , PRO A:95 , MET A:96 , TYR A:97 , ASN A:98 , PHE A:99 , SER A:140 , ARG A:141 , GLY A:142 , GLY A:143 , HIS A:145 , HOH A:498 , HOH A:630 , LEU B:51 , ARG B:60BINDING SITE FOR RESIDUE FMN A 202
2AC2SOFTWARELEU A:51 , SER B:10 , SER B:16 , GLN B:17 , SER B:18 , PRO B:95 , MET B:96 , TYR B:97 , ASN B:98 , PHE B:99 , SER B:140 , ARG B:141 , GLY B:142 , GLY B:143 , HIS B:145 , HOH B:468BINDING SITE FOR RESIDUE FMN B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T5B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1T5B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T5B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T5B)

(-) Exons   (0, 0)

(no "Exon" information available for 1T5B)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:199
 aligned with AZOR_SALTY | P63462 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 
           AZOR_SALTY     1 MSKVLVLKSSILAGYSQSGQLTDYFIEQWREKHVADEITVRDLAANPVPVLDGELVGAMRPGDAPLTPRQQDALALSDELIAELKAHDVIVIAAPMYNFNIPTQLKNYFDLIARAGITFRYTEKGPEGLVTGKRAVVLSSRGGIHKDTPTDLIAPYLKVFLGFIGITDVNFVFAEGIAYGPEVAAKAQADAKAAIDSVVAA 201
               SCOP domains d1t5ba_ A: ACP phosphodiesterase AcpD                                                                                                                                                                     SCOP domains
               CATH domains 1t5bA00 A:1-201  [code=3.40.50.360, no name defined]                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhh.--....hhhhhhhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhhhh.....eeee..eeee.....eeeeeee...........hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t5b A   1 MSKVLVLKSSILAGYSQSGQLTDYFIEQWREKHVADEITVRDLAANPVPVLDGELVGAMR--DAPLTPRQQDALALSDELIAELKAHDVIVIAAPMYNFNIPTQLKNYFDLIARAGITFRYTEKGPEGLVTGKRAVVLSSRGGIHKDTPTDLIAPYLKVFLGFIGITDVNFVFAEGIAYGPEVAAKAQADAKAAIDSVVAA 201
                                    10        20        30        40        50        60  |     70        80        90       100       110       120       130       140       150       160       170       180       190       200 
                                                                                      60 63                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:198
 aligned with AZOR_SALTY | P63462 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 
           AZOR_SALTY     1 MSKVLVLKSSILAGYSQSGQLTDYFIEQWREKHVADEITVRDLAANPVPVLDGELVGAMRPGDAPLTPRQQDALALSDELIAELKAHDVIVIAAPMYNFNIPTQLKNYFDLIARAGITFRYTEKGPEGLVTGKRAVVLSSRGGIHKDTPTDLIAPYLKVFLGFIGITDVNFVFAEGIAYGPEVAAKAQADAKAAIDSVVAA 201
               SCOP domains d1t5bb_ B: ACP phosphodiesterase AcpD                                                                                                                                                                     SCOP domains
               CATH domains 1t5bB00 B:1-201  [code=3.40.50.360, no name defined]                                                                                                                                                      CATH domains
           Pfam domains (1) -Flavodoxin_2-1t5bB01 B:2-198                                                                                                                                                                         --- Pfam domains (1)
           Pfam domains (2) -Flavodoxin_2-1t5bB02 B:2-198                                                                                                                                                                         --- Pfam domains (2)
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhh.---...hhhhhhhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhhhh.....eeee..eeee.....eeeeeee...........hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t5b B   1 MSKVLVLKSSILAGYSQSGQLTDYFIEQWREKHVADEITVRDLAANPVPVLDGELVGAMR---APLTPRQQDALALSDELIAELKAHDVIVIAAPMYNFNIPTQLKNYFDLIARAGITFRYTEKGPEGLVTGKRAVVLSSRGGIHKDTPTDLIAPYLKVFLGFIGITDVNFVFAEGIAYGPEVAAKAQADAKAAIDSVVAA 201
                                    10        20        30        40        50        60   |    70        80        90       100       110       120       130       140       150       160       170       180       190       200 
                                                                                      60  64
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Flavoprotein (71)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (AZOR_SALTY | P63462)
molecular function
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0008752    FMN reductase activity    Catalysis of the reaction: FMNH2 + NAD(P)+ = FMN + NAD(P)H + H+.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016652    oxidoreductase activity, acting on NAD(P)H, NAD(P) as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces NAD+ or NADP.
    GO:0016661    oxidoreductase activity, acting on other nitrogenous compounds as donors    Catalysis of an oxidation-reduction (redox) reaction in which a nitrogenous group, excluding NH and NH2 groups, acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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