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(-) Description

Title :  STRUCTURE OF IDP01002, A PUTATIVE OXIDOREDUCTASE FROM AND ESSENTIAL GENE OF SALMONELLA TYPHIMURIUM
 
Authors :  A. U. Singer, G. Minasov, E. Evdokimova, J. S. Brunzelle, M. Kudritska, A. M. Edwards, W. F. Anderson, A. Savchenko, Center For Structural Of Infectious Diseases (Csgid)
Date :  02 Oct 08  (Deposition) - 04 Nov 08  (Release) - 15 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (4x),B (4x)
Biol. Unit 2:  A  (4x)
Biol. Unit 3:  B  (4x)
Keywords :  Funded By The National Institute Of Allergy And Infectious Diseases Of Nih Contract Number Hhsn272200700058C, Predicted Oxidoreductase, Essential Gene, Salmonella, Molecular Replacement, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Kim, R. Flick, J. Brunzelle, A. Singer, E. Evdokimova, G. Brown, J. C. Joo, G. A. Minasov, W. F. Anderson, R. Mahadevan, A. Savchenko, A. F. Yakunin
Structural And Biochemical Studies Of Novel Aldo-Keto Reductases For The Biocatalytic Conversion Of 3-Hydroxybutanal To 1, 3-Butanediol.
Appl. Environ. Microbiol. 2017
PubMed-ID: 28130301  |  Reference-DOI: 10.1128/AEM.03172-16

(-) Compounds

Molecule 1 - PUTATIVE OXIDOREDUCTASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TVLIC
    Expression System Strain: BL21-GOLD(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: STM2406
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): A (4x)B (4x)
Biological Unit 2 (4x): A 
Biological Unit 3 (4x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 24)

Asymmetric Unit (5, 24)
No.NameCountTypeFull Name
1CAC2Ligand/IonCACODYLATE ION
2CL5Ligand/IonCHLORIDE ION
3EDO13Ligand/Ion1,2-ETHANEDIOL
4NA2Ligand/IonSODIUM ION
5ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 40)
No.NameCountTypeFull Name
1CAC4Ligand/IonCACODYLATE ION
2CL-1Ligand/IonCHLORIDE ION
3EDO36Ligand/Ion1,2-ETHANEDIOL
4NA-1Ligand/IonSODIUM ION
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 40)
No.NameCountTypeFull Name
1CAC4Ligand/IonCACODYLATE ION
2CL-1Ligand/IonCHLORIDE ION
3EDO36Ligand/Ion1,2-ETHANEDIOL
4NA-1Ligand/IonSODIUM ION
5ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 20)
No.NameCountTypeFull Name
1CAC4Ligand/IonCACODYLATE ION
2CL-1Ligand/IonCHLORIDE ION
3EDO16Ligand/Ion1,2-ETHANEDIOL
4NA-1Ligand/IonSODIUM ION
5ZN-1Ligand/IonZINC ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:155 , HIS A:159 , HOH A:765 , HOH A:767 , HOH A:770BINDING SITE FOR RESIDUE ZN A 333
02AC2SOFTWAREHIS A:138 , SER A:168 , GLN A:193 , CAC A:337BINDING SITE FOR RESIDUE NA A 334
03AC3SOFTWARESER A:222 , LEU A:224 , GLY A:226 , HOH A:572BINDING SITE FOR RESIDUE CL A 335
04AC4SOFTWAREHIS A:155 , HIS A:159 , HOH A:575BINDING SITE FOR RESIDUE CL A 336
05AC5SOFTWARETRP A:33 , TYR A:66 , HIS A:138 , ASN A:169 , PHE A:221 , NA A:334 , EDO A:342 , HOH A:771BINDING SITE FOR RESIDUE CAC A 337
06AC6SOFTWARELEU A:269 , ARG A:272 , GLU A:320 , EDO A:339 , HOH A:430 , ASN B:169BINDING SITE FOR RESIDUE EDO A 338
07AC7SOFTWAREARG A:272 , EDO A:338 , HOH A:443 , TYR B:170 , VAL B:203 , HOH B:782BINDING SITE FOR RESIDUE EDO A 339
08AC8SOFTWAREALA A:172 , ASP A:173 , ARG A:176 , HOH A:630BINDING SITE FOR RESIDUE EDO A 340
09AC9SOFTWAREALA A:257 , ASP A:258 , GLU A:261 , ARG A:331 , PHE A:332 , TYR B:15 , LYS B:24 , HOH B:772BINDING SITE FOR RESIDUE EDO A 341
10BC1SOFTWAREASN A:65 , TYR A:66 , TYR A:100 , HIS A:138 , CAC A:337 , HOH A:686 , HOH A:699BINDING SITE FOR RESIDUE EDO A 342
11BC2SOFTWAREARG A:17 , TRP A:110 , ASP A:141 , PRO A:142 , GLU A:143 , HOH A:395BINDING SITE FOR RESIDUE EDO A 343
12BC3SOFTWARETHR A:40 , ARG A:41 , HOH A:383 , ARG B:41BINDING SITE FOR RESIDUE EDO A 344
13BC4SOFTWARECYS A:75 , ASN A:76 , ARG A:79 , HOH A:480 , ARG B:79 , HOH B:733 , HOH B:827BINDING SITE FOR RESIDUE EDO A 345
14BC5SOFTWAREARG A:9 , GLU A:91 , TRP A:103 , ASP A:104 , HOH A:781BINDING SITE FOR RESIDUE EDO A 346
15BC6SOFTWAREHIS B:155 , HOH B:895 , HOH B:897 , HOH B:901BINDING SITE FOR RESIDUE ZN B 333
16BC7SOFTWARELYS B:97 , HIS B:138 , SER B:168 , GLN B:193 , CAC B:338BINDING SITE FOR RESIDUE NA B 334
17BC8SOFTWARESER B:222 , LEU B:224 , GLY B:226BINDING SITE FOR RESIDUE CL B 335
18BC9SOFTWARESER A:317 , HOH A:430 , LYS B:195 , HOH B:665BINDING SITE FOR RESIDUE CL B 336
19CC1SOFTWAREHIS B:155 , HIS B:159 , HOH B:637BINDING SITE FOR RESIDUE CL B 337
20CC2SOFTWARETRP B:33 , TYR B:66 , HIS B:138 , ASN B:169 , PHE B:221 , NA B:334BINDING SITE FOR RESIDUE CAC B 338
21CC3SOFTWAREALA B:172 , ASP B:173 , ARG B:176 , HOH B:771 , HOH B:852BINDING SITE FOR RESIDUE EDO B 339
22CC4SOFTWAREALA A:326 , TYR B:100 , THR B:101 , ARG B:139 , HOH B:550 , HOH B:577 , HOH B:638 , HOH B:693 , HOH B:884BINDING SITE FOR RESIDUE EDO B 340
23CC5SOFTWAREARG A:41 , THR B:39 , THR B:40 , ARG B:41 , ASN B:44 , HOH B:657 , HOH B:892BINDING SITE FOR RESIDUE EDO B 341
24CC6SOFTWAREARG A:272 , ARG A:273 , ASN A:313 , GLU B:200 , TRP B:202 , HOH B:579 , HOH B:782BINDING SITE FOR RESIDUE EDO B 342

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:67 -Pro A:68
2Pro A:68 -Pro A:69
3Gly B:67 -Pro B:68
4Pro B:68 -Pro B:69

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ERP)

(-) 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:312
 aligned with Q8ZNA1_SALTY | Q8ZNA1 from UniProtKB/TrEMBL  Length:332

    Alignment length:331
                                    11        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 
         Q8ZNA1_SALTY     2 IYQPDENRYHTMEYRRCGRSGVKLPAISLGLWHNFGDTTRVENSRALLQRAFDLGITHFDLANNYGPPPGSAECNFGRILQEDFLPWRDELIISTKAGYTMWDGPYGDWGSRKYLIASLDQSLKRMGLEYVDIFYHHRPDPETPLKETMKALDHLVRHGKALYVGISNYPADLARQAIDILEDLGTPCLIHQPKYSLFERWVEDGLLALLQEKGVGSIAFSPLAGGQLTDRYLNGIPEDSRAASGSRFLKPEQITADKLEKVRRLNELAARRGQKLSQMALAWVLRNDNVTSVLIGASKPSQIEDAVGMLANRRFSAAECAEIDAILEGRF 332
               SCOP domains d3erpa_ A: automated matches                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eee......eee.eeee.........hhhhhhhhhhhhhhh...eee.........hhhhhhhhhhhhhhhhhhhhhheeeeee.............hhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhh.eeee...hhhhh.hhhhh.-------------------.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhh......eeee...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3erp A   2 IYQPDENRYHTMEYRRCGRSGVKLPAISLGLWHNFGDTTRVENSRALLQRAFDLGITHFDLANNYGPPPGSAECNFGRILQEDFLPWRDELIISTKAGYTMWDGPYGDWGSRKYLIASLDQSLKRMGLEYVDIFYHHRPDPETPLKETMKALDHLVRHGKALYVGISNYPADLARQAIDILEDLGTPCLIHQPKYSLFERWVEDGLLALLQEKGVGSIAFSPLAGGQLTDRYLN-------------------ITADKLEKVRRLNELAARRGQKLSQMALAWVLRNDNVTSVLIGASKPSQIEDAVGMLANRRFSAAECAEIDAILEGRF 332
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231   |     -         -   |   261       271       281       291       301       311       321       331 
                                                                                                                                                                                                                                                                   235                 255                                                                             


Chain B from PDB  Type:PROTEIN  Length:306
 aligned with Q8ZNA1_SALTY | Q8ZNA1 from UniProtKB/TrEMBL  Length:332

    Alignment length:330
                                    11        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
         Q8ZNA1_SALTY     2 IYQPDENRYHTMEYRRCGRSGVKLPAISLGLWHNFGDTTRVENSRALLQRAFDLGITHFDLANNYGPPPGSAECNFGRILQEDFLPWRDELIISTKAGYTMWDGPYGDWGSRKYLIASLDQSLKRMGLEYVDIFYHHRPDPETPLKETMKALDHLVRHGKALYVGISNYPADLARQAIDILEDLGTPCLIHQPKYSLFERWVEDGLLALLQEKGVGSIAFSPLAGGQLTDRYLNGIPEDSRAASGSRFLKPEQITADKLEKVRRLNELAARRGQKLSQMALAWVLRNDNVTSVLIGASKPSQIEDAVGMLANRRFSAAECAEIDAILEGR 331
               SCOP domains d3erpb_ B: automated matches                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eee......eee.eeee.........hhhhhhhhhhhhhhh...eee.........hhhhhhhhhhhhhhhhhhhhhheeeeee.............hhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhh.eeee...hhhhh.....------------------------hhhhhhhhhhhhhhhh..hhhhhhhhhhh......eeee...hhhhhhhhhhhhhh...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3erp B   2 IYQPDENRYHTMEYRRCGRSGVKLPAISLGLWHNFGDTTRVENSRALLQRAFDLGITHFDLANNYGPPPGSAECNFGRILQEDFLPWRDELIISTKAGYTMWDGPYGDWGSRKYLIASLDQSLKRMGLEYVDIFYHHRPDPETPLKETMKALDHLVRHGKALYVGISNYPADLARQAIDILEDLGTPCLIHQPKYSLFERWVEDGLLALLQEKGVGSIAFSPLAGGQLTDRY------------------------DKLEKVRRLNELAARRGQKLSQMALAWVLRNDNVTSVLIGASKPSQIEDAVGMLANRRFSAAECAEIDAILEGR 331
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231 |       -         -      |261       271       281       291       301       311       321       331
                                                                                                                                                                                                                                                                 233                      258
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  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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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        Q8ZNA1_SALTY | Q8ZNA1: 5t79

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