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(-) Description

Title :  CRYSTAL STRUCTURE OF N-TERMINAL 40KD MUTL/A100P MUTANT PROTEIN COMPLEX WITH ADPNP AND ONE SODIUM
 
Authors :  X. Hu, M. Machius, W. Yang
Date :  19 Dec 02  (Deposition) - 10 Jun 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Dna Mismatch Repair, Mutl, Atpase, Rubidium, Replication, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Hu, M. Machius, W. Yang
Monovalent Cation Dependence And Preference Of Ghkl Atpases And Kinases
Febs Lett. V. 544 268 2003
PubMed-ID: 12782329  |  Reference-DOI: 10.1016/S0014-5793(03)00519-2

(-) Compounds

Molecule 1 - DNA MISMATCH REPAIR PROTEIN MUTL
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPWY1381
    Expression System StrainHMS174 (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL 40KD ATPASE FRAGMENT (LN40)
    GeneMUTL
    MutationYES
    Organism ScientificESCHERICHIA COLI K12
    Organism Taxid83333
    StrainK-12

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG1Ligand/IonMAGNESIUM ION
3NA1Ligand/IonSODIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3NA-1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:71 , ALA A:73 , ALA A:76 , GLY A:96 , PRO A:100 , ANP A:380BINDING SITE FOR RESIDUE NA A 390
2AC2SOFTWAREASN A:33 , ANP A:380 , HOH A:402 , HOH A:436BINDING SITE FOR RESIDUE MG A 370
3AC3SOFTWAREILE A:3 , GLU A:29 , ASN A:33 , ALA A:37 , ASP A:58 , GLY A:62 , ILE A:63 , ALA A:71 , THR A:77 , SER A:78 , LYS A:79 , GLY A:93 , PHE A:94 , ARG A:95 , GLY A:96 , GLU A:97 , ALA A:98 , LEU A:99 , PRO A:100 , THR A:143 , LYS A:307 , MG A:370 , NA A:390 , HOH A:397 , HOH A:435 , HOH A:437 , HOH A:446 , HOH A:516BINDING SITE FOR RESIDUE ANP A 380

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNA_MISMATCH_REPAIR_1PS00058 DNA mismatch repair proteins mutL / hexB / PMS1 signature.MUTL_ECO5793-99  1A:93-99
MUTL_ECOLI93-99  1A:93-99
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNA_MISMATCH_REPAIR_1PS00058 DNA mismatch repair proteins mutL / hexB / PMS1 signature.MUTL_ECO5793-99  2A:93-99
MUTL_ECOLI93-99  2A:93-99

(-) Exons   (0, 0)

(no "Exon" information available for 1NHJ)

(-) 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:333
 aligned with MUTL_ECO57 | Q8XDN4 from UniProtKB/Swiss-Prot  Length:615

    Alignment length:333
                              1                                                                                                                                                                                                                                                                                                                                          
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328   
           MUTL_ECO57     - --MPIQVLPPQLANQIAAGEVVERPASVVKELVENSLDAGATRIDIDIERGGAKLIRIRDNGCGIKKDELALALARHATSKIASLDDLEAIISLGFRGEALASISSVSRLTLTSRTAEQQEAWQAYAEGRDMDVTVKPAAHPVGTTLEVLDLFYNTPARRKFLRTEKTEFNHIDEIIRRIALARFDVTINLSHNGKIVRQYRAVPEGGQKERRLGAICGTAFLEQALAIEWQHGDLTLRGWVADPNHTTPALAEIQYCYVNGRMMRDRLINHAIRQACEDKLGADQQPAFVLYLEIDPHQVDVNVHPAKHEVRFHQSRLVHDFIYQGVLSVLQ 331
               SCOP domains d1nhja2 A:-2-216 DNA mismatch repair protein MutL                                                                                                                                                                         d1nhja1 A:217-331 DNA mismatch repair protein MutL                                                                  SCOP domains
               CATH domains --1nhjA01 A:1-216  [code=3.30.565.10, no name defined]                                                                                                                                                                    1nhjA02 A:217-330  [code=3.30.230.10, no name defined]                                                            - CATH domains
               Pfam domains ----------------------HATPase_c_3-1nhjA01 A:21-142                                                                                              ---------------------------------------------------------------------DNA_mis_repair-1nhjA02 A:212-331                                                                                         Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...eeeeee.hhhh.eeeeee.....hhhhhhhhh.........hhhhhh.........hhhhhhhh..eeeeeee......eeeeeee....eeeeeee....eeeeeee.....hhhhhh...hhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeee........hhhhhhhhhhhhhhhheeeeeeee..eeeeeeee.hhhh..hhhh.eeeee..ee..hhhhhhhhhhhhhh.........eeeeee.....ee..........ee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------DNA_MIS---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nhj A  -2 SHMPIQVLPPQLANQIAAGEVVERPASVVKELVENSLDAGATRIDIDIERGGAKLIRIRDNGCGIKKDELALALARHATSKIASLDDLEAIISLGFRGEALPSISSVSRLTLTSRTAEQQEAWQAYAEGRDMNVTVKPAAHPVGTTLEVLDLFYNTPARRKFLRTEKTEFNHIDEIIRRIALARFDVTINLSHNGKIVRQYRAVPEGGQKERRLGAICGTAFLEQALAIEWQHGDLTLRGWVADPNHTTPALAEIQYCYVNGRMMRDRLINHAIRQACEDKLGADQQPAFVLYLEIDPHQVDVNVHPAKHEVRFHQSRLVHDFIYQGVLSVLQ 331
                             ||      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328   
                             ||                                                                                                                                                                                                                                                                                                                                          
                            -1|                                                                                                                                                                                                                                                                                                                                          
                              1                                                                                                                                                                                                                                                                                                                                          

Chain A from PDB  Type:PROTEIN  Length:333
 aligned with MUTL_ECOLI | P23367 from UniProtKB/Swiss-Prot  Length:615

    Alignment length:333
                              1                                                                                                                                                                                                                                                                                                                                          
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328   
           MUTL_ECOLI     - --MPIQVLPPQLANQIAAGEVVERPASVVKELVENSLDAGATRIDIDIERGGAKLIRIRDNGCGIKKDELALALARHATSKIASLDDLEAIISLGFRGEALASISSVSRLTLTSRTAEQQEAWQAYAEGRDMNVTVKPAAHPVGTTLEVLDLFYNTPARRKFLRTEKTEFNHIDEIIRRIALARFDVTINLSHNGKIVRQYRAVPEGGQKERRLGAICGTAFLEQALAIEWQHGDLTLRGWVADPNHTTPALAEIQYCYVNGRMMRDRLINHAIRQACEDKLGADQQPAFVLYLEIDPHQVDVNVHPAKHEVRFHQSRLVHDFIYQGVLSVLQ 331
               SCOP domains d1nhja2 A:-2-216 DNA mismatch repair protein MutL                                                                                                                                                                         d1nhja1 A:217-331 DNA mismatch repair protein MutL                                                                  SCOP domains
               CATH domains --1nhjA01 A:1-216  [code=3.30.565.10, no name defined]                                                                                                                                                                    1nhjA02 A:217-330  [code=3.30.230.10, no name defined]                                                            - CATH domains
               Pfam domains ----------------------HATPase_c_3-1nhjA01 A:21-142                                                                                              ---------------------------------------------------------------------DNA_mis_repair-1nhjA02 A:212-331                                                                                         Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...eeeeee.hhhh.eeeeee.....hhhhhhhhh.........hhhhhh.........hhhhhhhh..eeeeeee......eeeeeee....eeeeeee....eeeeeee.....hhhhhh...hhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeee........hhhhhhhhhhhhhhhheeeeeeee..eeeeeeee.hhhh..hhhh.eeeee..ee..hhhhhhhhhhhhhh.........eeeeee.....ee..........ee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------------------------------------------------------------------------------------DNA_MIS---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nhj A  -2 SHMPIQVLPPQLANQIAAGEVVERPASVVKELVENSLDAGATRIDIDIERGGAKLIRIRDNGCGIKKDELALALARHATSKIASLDDLEAIISLGFRGEALPSISSVSRLTLTSRTAEQQEAWQAYAEGRDMNVTVKPAAHPVGTTLEVLDLFYNTPARRKFLRTEKTEFNHIDEIIRRIALARFDVTINLSHNGKIVRQYRAVPEGGQKERRLGAICGTAFLEQALAIEWQHGDLTLRGWVADPNHTTPALAEIQYCYVNGRMMRDRLINHAIRQACEDKLGADQQPAFVLYLEIDPHQVDVNVHPAKHEVRFHQSRLVHDFIYQGVLSVLQ 331
                             ||      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328   
                            -1|                                                                                                                                                                                                                                                                                                                                          
                              1                                                                                                                                                                                                                                                                                                                                          

   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, 2)

Asymmetric Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: S5 (103)

(-) Gene Ontology  (13, 18)

Asymmetric Unit(hide GO term definitions)
Chain A   (MUTL_ECOLI | P23367)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0030983    mismatched DNA binding    Interacting selectively and non-covalently with double-stranded DNA containing one or more mismatches.
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0006298    mismatch repair    A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.
    GO:0000018    regulation of DNA recombination    Any process that modulates the frequency, rate or extent of DNA recombination, a DNA metabolic process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents.
cellular component
    GO:0032300    mismatch repair complex    Any complex formed of proteins that act in mismatch repair.

Chain A   (MUTL_ECO57 | Q8XDN4)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0030983    mismatched DNA binding    Interacting selectively and non-covalently with double-stranded DNA containing one or more mismatches.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0006298    mismatch repair    A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MUTL_ECO57 | Q8XDN41nhh 1nhi
        MUTL_ECOLI | P233671b62 1b63 1bkn 1nhh 1nhi 1x9z 5akb 5akc 5akd

(-) Related Entries Specified in the PDB File

1b63 1nhh 1nhi