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(-) Description

Title :  HUMAN PARAPLEGIN, AAA DOMAIN IN COMPLEX WITH ADP
 
Authors :  T. Karlberg, L. Lehtio, C. H. Arrowsmith, H. Berglund, R. D. Busam, R. Co L. G. Dahlgren, A. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hamma M. D. Herman, I. Johansson, A. Kallas, T. Kotenyova, M. Moche, M. E. Nil P. Nordlund, T. Nyman, J. Persson, C. Sagemark, M. Sundstrom, A. G. Tho L. Tresauges, S. Van Den Berg, J. Weigelt, M. Welin, L. Holmberg-Sch Structural Genomics Consortium (Sgc)
Date :  16 Aug 07  (Deposition) - 11 Sep 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.22
Chains :  Asym./Biol. Unit :  A
Keywords :  Aaa+, Spg7, Protease, Adp, Structural Genomics, Structural Genomics Consortium, Sgc, Atp-Binding, Nucleotide-Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Karlberg, S. Van Den Berg, M. Hammarstrom, J. Sagemark, I. Johansson, L. Holmberg-Schiavone, H. Schuler
Crystal Structure Of The Atpase Domain Of The Human Aaa+ Protein Paraplegin/Spg7.
Plos One V. 4 E6975 2009
PubMed-ID: 19841671  |  Reference-DOI: 10.1371/JOURNAL.PONE.0006975

(-) Compounds

Molecule 1 - PARAPLEGIN
    ChainsA
    EC Number3.4.24.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC-BSA4
    Expression System StrainBL21(DE3) GOLD PRARE2
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneSPG7
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSPASTIC PARAPLEGIA PROTEIN 7
    TissueBRAIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:27 , HOH A:28 , HOH A:54 , HOH A:55 , ASP A:310 , ALA A:312 , PRO A:351 , GLY A:352 , CYS A:353 , GLY A:354 , LYS A:355 , THR A:356 , LEU A:357 , ARG A:389 , SER A:392 , HIS A:492 , GLY A:518 , ALA A:519BINDING SITE FOR RESIDUE ADP A 700

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QZ4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:401 -Pro A:402

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Asymmetric/Biological Unit (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_063607G349SSPG7_HUMANDisease (SPG7)141659620AG349S
2UniProtVAR_063608R486QSPG7_HUMANPolymorphism111475461AR486Q
3UniProtVAR_017433T503ASPG7_HUMANPolymorphism2292954AT503A
4UniProtVAR_063609A510VSPG7_HUMANDisease (SPG7)61755320AA510V
5UniProtVAR_063610F545LSPG7_HUMANPolymorphism  ---AF545L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QZ4)

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002687041aENSE00000946159chr16:89574811-89575008198SPG7_HUMAN1-61610--
1.2ENST000002687042ENSE00001401252chr16:89576898-89577000103SPG7_HUMAN62-96350--
1.3ENST000002687043ENSE00001414953chr16:89579356-8957944590SPG7_HUMAN96-126310--
1.6bENST000002687046bENSE00001408619chr16:89590414-89590655242SPG7_HUMAN126-206810--
1.7bENST000002687047bENSE00001420681chr16:89592737-89592876140SPG7_HUMAN207-253470--
1.8ENST000002687048ENSE00001409998chr16:89595885-89595987103SPG7_HUMAN253-287350--
1.9ENST000002687049ENSE00001418083chr16:89597091-89597216126SPG7_HUMAN288-329421A:304-32926
1.10ENST0000026870410ENSE00001427640chr16:89598312-89598474163SPG7_HUMAN330-384551A:330-384 (gaps)55
1.11ENST0000026870411ENSE00001401248chr16:89598871-89599044174SPG7_HUMAN384-442591A:384-442 (gaps)59
1.13ENST0000026870413ENSE00001410114chr16:89611056-89611180125SPG7_HUMAN442-483421A:442-48342
1.14ENST0000026870414ENSE00001434018chr16:89613066-89613168103SPG7_HUMAN484-518351A:484-51835
1.15aENST0000026870415aENSE00001427588chr16:89614411-89614521111SPG7_HUMAN518-555381A:518-555 (gaps)38
1.21bENST0000026870421bENSE00001359493chr16:89616902-89617017116SPG7_HUMAN555-593391A:555-5595
1.22bENST0000026870422bENSE00001402484chr16:89619387-89619543157SPG7_HUMAN594-646530--
1.24bENST0000026870424bENSE00001419909chr16:89620202-89620368167SPG7_HUMAN646-701560--
1.25ENST0000026870425ENSE00001429395chr16:89620894-8962097178SPG7_HUMAN702-727260--
1.26ENST0000026870426ENSE00001283443chr16:89623295-89624174880SPG7_HUMAN728-795680--

(-) 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
(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:223
 aligned with SPG7_HUMAN | Q9UQ90 from UniProtKB/Swiss-Prot  Length:795

    Alignment length:256
                                   313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553      
           SPG7_HUMAN   304 KGVSFKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGTTDHVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRLAELTPGFSGADIANICNEAALHAAREGHTSVHTLNFEYAVERVLAGTAKK 559
               SCOP domains d2qz4a_ A: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2qz4A01 A:304-479 P-loop cont      aining nucleotide triphosphate hydrolases                                                                                                    2qz4A02 A:480-556  [code=1.10.8.60, no name defined]                         --- CATH domains
               Pfam domains -----------------------------      ------AAA-2qz4A01 A:345-479                                                                                                                  ----------------------------------------------------        -Peptidase_M41-2qz4A Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhh..------.....eeeee.....hhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhhhhhh..eeeeee..-------------------hhhhhhhhhhhhh......eeeeeee.hhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhh....hhhhhhhhhhhh....hhhhhhhhhhhhhh.--------....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------S----------------------------------------------------------------------------------------------------------------------------------------Q----------------A------V----------------------------------L-------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.9  PDB: A:304-329  Exon 1.10  PDB: A:330-384 (gaps) UniProt: 330-384      ---------------------------------------------------------Exon 1.13  PDB: A:442-483 UniProt: 442-483Exon 1.14  PDB: A:484-518          ------------------------------------1.21b Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------Exon 1.11  PDB: A:384-442 (gaps) UniProt: 384-442          ---------------------------------------------------------------------------Exon 1.15a  PDB: A:518-555 (gaps)     ---- Transcript 1 (2)
                 2qz4 A 304 MGVSFKDVAGMHEAKLEVREFVDYLKSPE------AKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGAEFVEVIGGLGAARVRSLFKEARARAPCIVYIDEI-------------------EQTLNQLLVEMDGMGTTDHVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRLAELTPGFSGADIANICNEAALH--------VHTLNFEYAVERVLAGTAKK 559
                                   313       323        |-     | 343       353       363       373       383       393       403      |  -         -      |433       443       453       463       473       483       493       503       513       523       | -      |543       553      
                                                      332    339                                                                    410                 430                                                                                                  531      540                   

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SPG7_HUMAN | Q9UQ90)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004176    ATP-dependent peptidase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the hydrolysis of peptide bonds.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    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:0051082    unfolded protein binding    Interacting selectively and non-covalently with an unfolded protein.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0008089    anterograde axonal transport    The directed movement of organelles or molecules along microtubules from the cell body toward the cell periphery in nerve cell axons.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0007005    mitochondrion organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:1904115    axon cytoplasm    Any cytoplasm that is part of a axon.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031966    mitochondrial membrane    Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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