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(-) Description

Title :  CRYSTAL STRUCTURE OF DNA HELICASE REPA IN COMPLEX WITH SULFATE AT 1.95 A RESOLUTION
 
Authors :  H. Xu, N. Strater, W. Schroeder, C. Bottcher, K. Ludwig, W. Saenger
Date :  07 Jan 03  (Deposition) - 29 Apr 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Replicative Dna Helicase Structural Changes, Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Xu, N. Strater, W. Schroder, C. Bottcher, K. Ludwig, W. Saenger
Structure Of Dna Helicase Repa In Complex With Sulfate At 1. 95 A Resolution Implicates Structural Changes To An "Open Form.
Acta Crystallogr. , Sect. D V. 59 815 2003
PubMed-ID: 12777796  |  Reference-DOI: 10.1107/S0907444903004025

(-) Compounds

Molecule 1 - REGULATORY PROTEIN REPA
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMS119EH
    Expression System Strain: PGZ18
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: REPA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:40 , ALA A:41 , GLY A:42 , LYS A:43 , SER A:44 , HIS A:179 , HOH A:1315 , HOH A:1352 , HOH A:1378 , HOH A:1423BINDING SITE FOR RESIDUE SO4 A 1300
2AC2SOFTWAREGLY B:40 , ALA B:41 , GLY B:42 , LYS B:43 , SER B:44 , HIS B:179 , HOH B:1403 , HOH B:1434 , HOH B:1464 , HOH B:1489BINDING SITE FOR RESIDUE SO4 B 1310
3AC3SOFTWAREGLY C:40 , ALA C:41 , GLY C:42 , LYS C:43 , SER C:44 , HIS C:179 , HOH C:1344 , HOH C:1394 , HOH C:1405BINDING SITE FOR RESIDUE SO4 C 1320

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asp A:140 -Thr A:141
2Asp B:140 -Thr B:141
3Asp C:140 -Thr C:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NLF)

(-) 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:254
 aligned with REPJ_ECOLX | P20356 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:274
                                    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    
           REPJ_ECOLX     2 ATHKPINILEAFAAAPPPLDYVLPNMVAGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAEDPPTAIHHRLHALGAHLSAEERQAVADGLLIQPLIGSLPNIMAPEWFDGLKRAAEGRRLMVLDTLRRFHIEEENASGPMAQVIGRMEAIAADTGCSIVFLHHASKGAAMMGAGDQQQASRGSSVLVDNIRWQSYLSSMTSAEAEEWGVDDDQRRFFVRFGVSKANYGAPFADRWFRRHDGGVLKPAVLERQRKSKGVP 275
               SCOP domains d1nlfa_ A: Hexameric replicative helicase repA                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1nlfA00 A:2-275 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhh......eee..ee...eeeeee....hhhhhhhhhhhhhhh..............eeeee...hhhhhhhhhhhhhh..hhhhhhhhhhheee...........hhhhhhhhhhhhh...eeeeehhhhhh.....hhhhhhhhhhhhhhhhhhhh.eeeeeee.--------------------.hhhhh..eeeeee.hhhhhhhh.....hhh.eeeeeeee.........eeeee.hhh.eee............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nlf A   2 ATHKPINILEAFAAAPPPLDYVLPNMVAGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAEDPPTAIHHRLHALGAHLSAEERQAVADGLLIQPLIGSLPNIMAPEWFDGLKRAAEGRRLMVLDTLRRFHIEEENASGPMAQVIGRMEAIAADTGCSIVFLHHA--------------------VLVDNIRWQSYLSSMTSAEAEEWGVDDDQRRFFVRFGVSKANYGAPFADRWFRRHDGGVLKPAVLERQRKSKGVP 275
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171        |-         -       201       211       221       231       241       251       261       271    
                                                                                                                                                                                                            180                  201                                                                          


Chain B from PDB  Type:PROTEIN  Length:254
 aligned with REPJ_ECOLX | P20356 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:274
                                    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    
           REPJ_ECOLX     2 ATHKPINILEAFAAAPPPLDYVLPNMVAGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAEDPPTAIHHRLHALGAHLSAEERQAVADGLLIQPLIGSLPNIMAPEWFDGLKRAAEGRRLMVLDTLRRFHIEEENASGPMAQVIGRMEAIAADTGCSIVFLHHASKGAAMMGAGDQQQASRGSSVLVDNIRWQSYLSSMTSAEAEEWGVDDDQRRFFVRFGVSKANYGAPFADRWFRRHDGGVLKPAVLERQRKSKGVP 275
               SCOP domains d1nlfb_ B: Hexameric replicative helicase repA                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1nlfB00 B:2-275 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhh......eee..ee...eeeeee....hhhhhhhhhhhhhhh..............eeeee...hhhhhhhhhhhhhh..hhhhhhhhhhheee...........hhhhhhhhhhhhh...eeeeehhhhhh.....hhhhhhhhhhhhhhhhhhhh.eeeeeee.--------------------.......eeeeeee.hhhhhhhh.....hhh.eeeeeeee.........eeeee.hhh.ee.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nlf B   2 ATHKPINILEAFAAAPPPLDYVLPNMVAGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAEDPPTAIHHRLHALGAHLSAEERQAVADGLLIQPLIGSLPNIMAPEWFDGLKRAAEGRRLMVLDTLRRFHIEEENASGPMAQVIGRMEAIAADTGCSIVFLHHA--------------------VLVDNIRWQSYLSSMTSAEAEEWGVDDDQRRFFVRFGVSKANYGAPFADRWFRRHDGGVLKPAVLERQRKSKGVP 275
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171        |-         -       201       211       221       231       241       251       261       271    
                                                                                                                                                                                                            180                  201                                                                          


Chain C from PDB  Type:PROTEIN  Length:254
 aligned with REPJ_ECOLX | P20356 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:274
                                    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    
           REPJ_ECOLX     2 ATHKPINILEAFAAAPPPLDYVLPNMVAGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAEDPPTAIHHRLHALGAHLSAEERQAVADGLLIQPLIGSLPNIMAPEWFDGLKRAAEGRRLMVLDTLRRFHIEEENASGPMAQVIGRMEAIAADTGCSIVFLHHASKGAAMMGAGDQQQASRGSSVLVDNIRWQSYLSSMTSAEAEEWGVDDDQRRFFVRFGVSKANYGAPFADRWFRRHDGGVLKPAVLERQRKSKGVP 275
               SCOP domains d1nlfc_ C: Hexameric replicative helicase repA                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1nlfC00 C:2-275 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                               CATH domains
           Pfam domains (1) ---AAA_25-1nlfC01 C:5-180                                                                                                                                                          ----------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---AAA_25-1nlfC02 C:5-180                                                                                                                                                          ----------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ---AAA_25-1nlfC03 C:5-180                                                                                                                                                          ----------------------------------------------------------------------------------------------- Pfam domains (3)
         Sec.struct. author ......hhhhhhhh......eee..ee...eeeeee....hhhhhhhhhhhhhhh..............eeeee...hhhhhhhhhhhhhh..hhhhhhhhhhheee...........hhhhhhhhhhhhh...eeeeehhhhhh.....hhhhhhhhhhhhhhhhhhhh.eeeeeee.--------------------.......eeeeeee.hhhhhhhh.....hhh.eeeeeeee.........eeeee.hhh.ee.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nlf C   2 ATHKPINILEAFAAAPPPLDYVLPNMVAGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAEDPPTAIHHRLHALGAHLSAEERQAVADGLLIQPLIGSLPNIMAPEWFDGLKRAAEGRRLMVLDTLRRFHIEEENASGPMAQVIGRMEAIAADTGCSIVFLHHA--------------------VLVDNIRWQSYLSSMTSAEAEEWGVDDDQRRFFVRFGVSKANYGAPFADRWFRRHDGGVLKPAVLERQRKSKGVP 275
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171        |-         -       201       211       221       231       241       251       261       271    
                                                                                                                                                                                                            180                  201
   Legend:   → Mismatch (orange background)
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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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (REPJ_ECOLX | P20356)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0006276    plasmid maintenance    The maintenance of the integrity of extrachromosomal plasmid DNA; includes processes that ensure plasmids are retained in the daughter cells after cell division.

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 Related Entries

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UniProtKB/Swiss-Prot
        REPJ_ECOLX | P20356: 1g8y 1olo

(-) Related Entries Specified in the PDB File

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