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(-) Description

Title :  STRUCTURE OF THE C DOMAIN OF SYNAPSIN IA FROM BOVINE BRAIN WITH CALCIUM ATP-GAMMA-S BOUND
 
Authors :  L. Esser, C. Wang, J. Deisenhofer
Date :  06 Sep 97  (Deposition) - 18 Mar 98  (Release) - 15 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Synapse, Phosphorylation, Synapsin Ia C-Domain, Atp-Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Esser, C. R. Wang, M. Hosaka, C. S. Smagula, T. C. Sudhof, J. Deisenhofer
Synapsin I Is Structurally Similar To Atp-Utilizing Enzymes
Embo J. V. 17 977 1998
PubMed-ID: 9463376  |  Reference-DOI: 10.1093/EMBOJ/17.4.977
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SYNAPSIN IA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSYB21
    Expression System Strain: DH5-ALPHA
    Expression System Taxid: 562
    Expression System Vector: PGEX-CS
    Fragment: C DOMAIN
    Organism Common: CATTLE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1AGS2Ligand/IonPHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
2CA2Ligand/IonCALCIUM ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1AGS4Ligand/IonPHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
2CA-1Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:373 , GLU A:386 , AGS A:800BINDING SITE FOR RESIDUE CA A 801
2AC2SOFTWAREGLU B:373 , GLU B:386 , AGS B:800BINDING SITE FOR RESIDUE CA B 801
3AC3SOFTWARELYS A:225 , ILE A:247 , LYS A:269 , HIS A:274 , SER A:275 , GLY A:276 , LYS A:279 , GLU A:305 , PRO A:306 , PHE A:307 , ILE A:308 , GLU A:373 , LEU A:375 , ILE A:385 , CA A:801BINDING SITE FOR RESIDUE AGS A 800
4AC4SOFTWAREVAL B:267 , LYS B:269 , HIS B:274 , SER B:275 , GLY B:276 , LYS B:279 , GLU B:305 , PRO B:306 , PHE B:307 , ILE B:308 , ASP B:313 , GLU B:373 , LEU B:375 , GLU B:386 , CA B:801BINDING SITE FOR RESIDUE AGS B 800

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ile A:213 -Asn A:214
2Tyr A:264 -Pro A:265
3Ile B:213 -Asn B:214
4Tyr B:264 -Pro B:265

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SYNAPSIN_2PS00416 Synapsins signature 2.SYN1_BOVIN271-281
 		  2A:271-281
B:271-281
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SYNAPSIN_2PS00416 Synapsins signature 2.SYN1_BOVIN271-281
 		  4A:271-281
B:271-281

(-) Exons   (0, 0)

(no "Exon" information available for 1AUX)

(-) 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:292
 aligned with SYN1_BOVIN | P17599 from UniProtKB/Swiss-Prot  Length:706

    Alignment length:306
                                   121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411      
           SYN1_BOVIN   112 AARVLLVIDEPHTDWAKYFKGKKIHGEIDIKVEQAEFSDLNLVAHANGGFSVDMEVLRNGVKVVRSLKPDFVLIRQHAFSMARNGDYRSLVIGLQYAGIPSINSLHSVYNFCDKPWVFAQMVRLHKKLGTEEFPLINQTFYPNHKEMLSSTTYPVVVKMGHAHSGMGKVKVDNQHDFQDIASVVALTKTYATTEPFIDAKYDVRIQKIGQNYKAYMRTSVSGNWKTNTGSAMLEQIAMSDRYKLWVDTCSEIFGGLDICAVEALHGKDGRDHIIQVVGSSMPLIGDHQDEDKQLIVELVVNKMAQA 417
               SCOP domains d1auxa1 A:112-213 Synapsin I                                                                          d1auxa2 A:214-417 Synapsin                                                                                                                                                                                   SCOP domains
               CATH domains 1auxA02 A:112-214,A:394-406  [code=3.40.50.20, no name defined]                                        1auxA03 A:215-247,A:308-393      1auxA01 A:248-307 ATP-grasp fold, A domain                  1auxA03 A:215-247,A:30              8-393 ATP-grasp fold, B domain                    1auxA02      ----------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee......hhhh.....hhh...eeeeee.hhheeeee.....eeeee..........eee...eeee.............hhhhhhhhhh..eee..hhhhhhhh.hhhhhhhhhhhhhhh.........eeee.............eeeee........eeee..hhhhhhhhhhhhhh...eeeee...eeeeeeeeee..eeeeeee.--------------.eee...hhhhhhhhhhhhhhh...eeeeeeeee....eeeeeee..........hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------SYNAPSIN_2 ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1aux A 112 AARVLLVIDEPHTDWAKYFKGKKIHGEIDIKVEQAEFSDLNLVAHANGGFSVDMEVLRNGVKVVRSLKPDFVLIRQHAFSMARNGDYRSLVIGLQYAGIPSINSLHSVYNFCDKPWVFAQMVRLHKKLGTEEFPLINQTFYPNHKEMLSSTTYPVVVKMGHAHSGMGKVKVDNQHDFQDIASVVALTKTYATTEPFIDAKYDVRIQKIGQNYKAYMRT--------------LEQIAMSDRYKLWVDTCSEIFGGLDICAVEALHGKDGRDHIIEVVGSSMPLIGDHQDEDKQLIVELVVNKMAQA 417
                                   121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       | -         -  |    351       361       371       381       391       401       411      
                                                                                                                                                                                                                                                   329            344                                                                         


Chain B from PDB  Type:PROTEIN  Length:292
 aligned with SYN1_BOVIN | P17599 from UniProtKB/Swiss-Prot  Length:706

    Alignment length:306
                                   121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411      
           SYN1_BOVIN   112 AARVLLVIDEPHTDWAKYFKGKKIHGEIDIKVEQAEFSDLNLVAHANGGFSVDMEVLRNGVKVVRSLKPDFVLIRQHAFSMARNGDYRSLVIGLQYAGIPSINSLHSVYNFCDKPWVFAQMVRLHKKLGTEEFPLINQTFYPNHKEMLSSTTYPVVVKMGHAHSGMGKVKVDNQHDFQDIASVVALTKTYATTEPFIDAKYDVRIQKIGQNYKAYMRTSVSGNWKTNTGSAMLEQIAMSDRYKLWVDTCSEIFGGLDICAVEALHGKDGRDHIIQVVGSSMPLIGDHQDEDKQLIVELVVNKMAQA 417
               SCOP domains d1auxb1 B:112-213 Synapsin I                                                                          d1auxb2 B:214-417 Synapsin                                                                                                                                                                                   SCOP domains
               CATH domains 1auxB02 B:112-214,B:394-406  [code=3.40.50.20, no name defined]                                        1auxB03 B:215-247,B:308-393      1auxB01 B:248-307 ATP-grasp fold, A domain                  1auxB03 B:215-247,B:30              8-393 ATP-grasp fold, B domain                    1auxB02      ----------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee......hhhh.....hhh...eeeeee.hhheeeee.....eeeee..........eee...eeee.............hhhhhhhhhh..eee..hhhhhhhh.hhhhhhhhhhhhhhh.........eeee..hhh........eeeee........eeee..hhhhhhhhhhhhhh...eeeee...eeeeeeeeee..eeeeeee.--------------.eee...hhhhhhhhhhhhhhh...eeeeeeeee....eeeeeee..........hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------SYNAPSIN_2 ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1aux B 112 AARVLLVIDEPHTDWAKYFKGKKIHGEIDIKVEQAEFSDLNLVAHANGGFSVDMEVLRNGVKVVRSLKPDFVLIRQHAFSMARNGDYRSLVIGLQYAGIPSINSLHSVYNFCDKPWVFAQMVRLHKKLGTEEFPLINQTFYPNHKEMLSSTTYPVVVKMGHAHSGMGKVKVDNQHDFQDIASVVALTKTYATTEPFIDAKYDVRIQKIGQNYKAYMRT--------------LEQIAMSDRYKLWVDTCSEIFGGLDICAVEALHGKDGRDHIIEVVGSSMPLIGDHQDEDKQLIVELVVNKMAQA 417
                                   121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       | -         -  |    351       361       371       381       391       401       411      
                                                                                                                                                                                                                                                   329            344
   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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1AUX)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SYN1_BOVIN | P17599)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
biological process
    GO:0007269    neurotransmitter secretion    The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium regualated exocytosis during synaptic transmission.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
    GO:0008021    synaptic vesicle    A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.

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  1aux
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 Related Entries

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

UniProtKB/Swiss-Prot
        SYN1_BOVIN | P17599: 1auv

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