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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ASPARTATE AMINOTRANSFERASE (YP_354942.1) FROM RHODOBACTER SPHAEROIDES 2.4.1 AT 2.15 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  30 Jun 10  (Deposition) - 04 Aug 10  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of An Aspartate Aminotransferase (Yp_354942. 1) From Rhodobacter Sphaeroides 2. 4. 1 At 2. 15 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ASPARTATE AMINOTRANSFERASE
    Chains: A, B
    EC Number: 2.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RHOS4_34730, RSP_3437
    Organism Common: TBD
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 272943
    Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 32)

Asymmetric/Biological Unit (6, 32)
No.NameCountTypeFull Name
1CL11Ligand/IonCHLORIDE ION
2CSD2Mod. Amino Acid3-SULFINOALANINE
3GOL8Ligand/IonGLYCEROL
4LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
5MSE8Mod. Amino AcidSELENOMETHIONINE
6PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:189 , TYR A:338 , ARG A:380BINDING SITE FOR RESIDUE CL A 501
02AC2SOFTWAREPRO A:344 , LYS A:345 , ARG B:139BINDING SITE FOR RESIDUE CL A 503
03AC3SOFTWAREHIS A:51 , ARG A:307 , ARG A:310BINDING SITE FOR RESIDUE CL A 504
04AC4SOFTWAREGLU A:75 , LEU A:80 , HOH A:697BINDING SITE FOR RESIDUE CL A 505
05AC5SOFTWAREARG A:284BINDING SITE FOR RESIDUE CL A 510
06AC6SOFTWAREPRO A:35 , ARG B:209BINDING SITE FOR RESIDUE CL A 511
07AC7SOFTWAREPRO A:151 , GLN A:153 , ASP A:167 , HOH A:642 , HOH A:750 , HOH B:662BINDING SITE FOR RESIDUE GOL A 513
08AC8SOFTWAREALA A:159 , ARG A:323 , HOH A:607BINDING SITE FOR RESIDUE GOL A 514
09AC9SOFTWARELYS A:176 , ARG A:209BINDING SITE FOR RESIDUE GOL A 515
10BC1SOFTWARESER A:62 , GLN A:66 , HOH A:735 , HOH A:994 , PHE B:58BINDING SITE FOR RESIDUE GOL A 516
11BC2SOFTWAREGLU A:161 , THR A:162 , SER A:196 , ALA A:228 , SER A:229 , GLN A:334BINDING SITE FOR RESIDUE GOL A 519
12BC3SOFTWAREGLU A:161 , ALA A:226 , ARG A:315 , THR A:332 , GLN A:334 , HOH A:540BINDING SITE FOR RESIDUE PEG A 520
13BC4SOFTWAREALA A:72 , ALA A:286 , GLY A:287 , SER B:257 , GLY B:258 , ARG B:260 , HOH B:1137BINDING SITE FOR RESIDUE CL B 502
14BC5SOFTWAREHIS B:51 , ARG B:307 , ARG B:310BINDING SITE FOR RESIDUE CL B 506
15BC6SOFTWAREGLU B:75 , ASP B:79 , LEU B:80 , HOH B:665BINDING SITE FOR RESIDUE CL B 507
16BC7SOFTWAREHOH A:867 , ARG B:284 , HOH B:973BINDING SITE FOR RESIDUE CL B 508
17BC8SOFTWAREASN B:189 , TYR B:338 , ARG B:380BINDING SITE FOR RESIDUE CL B 509
18BC9SOFTWAREGLU B:161 , THR B:162 , SER B:196 , ALA B:228 , SER B:229 , GLN B:334BINDING SITE FOR RESIDUE GOL B 512
19CC1SOFTWAREHOH A:612 , HOH A:1054 , PRO B:151 , GLN B:153 , ASP B:167 , HOH B:577 , HOH B:637BINDING SITE FOR RESIDUE GOL B 517
20CC2SOFTWAREARG B:21 , SER B:23 , SER B:229 , TYR B:230 , HOH B:550BINDING SITE FOR RESIDUE GOL B 518

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Gln A:132 -Pro A:133
2Asn A:186 -Pro A:187
3Asn A:189 -Pro A:190
4Gln B:132 -Pro B:133
5Asn B:186 -Pro B:187
6Asn B:189 -Pro B:190

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NRA)

(-) 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:390
 aligned with Q3IWP3_RHOS4 | Q3IWP3 from UniProtKB/TrEMBL  Length:406

    Alignment length:405
                                    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       341       351       361       371       381       391       401     
         Q3IWP3_RHOS4     2 SIEAKFKKLGTDNAPGQEVRQSAAGLEALIRGAPIEGRPVDFSHGDVDAHEPTPGAFDLFSAGVQSGGVQAYTEYRGDLGIRDLLAPRLAAFTGAPVDARDGLIITPGTQGALFLAVAATVARGDKVAIVQPDYFANRKLVEFFEGEMVPVQLDYVSADETRAGLDLTGLEEAFKAGARVFLFSNPNNPAGVVYSAEEIGQIAALAARYGATVIADQLYSRLRYAGASYTHLRAEAAVDAENVVTIMGPSKTESLSGYRLGVAFGSRAIIARMEKLQAIVSLRAAGYSQAVLRGWFDEAPGWMEDRIARHQAIRDELLHVLRGCEGVFARTPQAGSYLFPRLPKLAVAPAEFVKILRLQAGVVVTPGTEFSPHTADSVRLNFSQDHEAAVAAARRIVTLVERYRA 406
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh..---------------..............ee.............hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh........eeeehhhhhhhhhhhhh......eeeeee...hhhhhhhhhh..eeeeee.............hhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhh.eeeee..............hhhhh...hhh.eeeee.......hhhhh.eeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.............ee.........hhhhhhhhhhhhhhee.ee.hhh.......eeee...hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nra A   2 SIEAKFKKLG---------------LEALIRGAPIEGRPVDFSHGDVDAHEPTPGAFDLFSAGVQSGGVQAYTEYRGDLGIRDLLAPRLAAFTGAPVDARDGLIITPGTQGALFLAVAATVARGDKVAIVQPDYFANRKLVEFFEGEmVPVQLDYVSADETRAGLDLTGLEEAFKAGARVFLFSNPNNPAGVVYSAEEIGQIAALAARYGATVIADQLYSRLRYAGASYTHLRAEAAVDAENVVTImGPSkTESLSGYRLGVAFGSRAIIARmEKLQAIVSLRAAGYSQAVLRGWFDEAPGWmEDRIARHQAIRDELLHVLRGcEGVFARTPQAGSYLFPRLPKLAVAPAEFVKILRLQAGVVVTPGTEFSPHTADSVRLNFSQDHEAAVAAARRIVTLVERYRA 406
                                    11         -     |  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       341       351       361       371       381       391       401     
                                    11              27                                                                                                                       149-MSE                                                                                            248-MSE                   274-MSE                       304-MSE              325-CSD                                                                             
                                                                                                                                                                                                                                                                                    252-LLP                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:396
 aligned with Q3IWP3_RHOS4 | Q3IWP3 from UniProtKB/TrEMBL  Length:406

    Alignment length:405
                                    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       341       351       361       371       381       391       401     
         Q3IWP3_RHOS4     2 SIEAKFKKLGTDNAPGQEVRQSAAGLEALIRGAPIEGRPVDFSHGDVDAHEPTPGAFDLFSAGVQSGGVQAYTEYRGDLGIRDLLAPRLAAFTGAPVDARDGLIITPGTQGALFLAVAATVARGDKVAIVQPDYFANRKLVEFFEGEMVPVQLDYVSADETRAGLDLTGLEEAFKAGARVFLFSNPNNPAGVVYSAEEIGQIAALAARYGATVIADQLYSRLRYAGASYTHLRAEAAVDAENVVTIMGPSKTESLSGYRLGVAFGSRAIIARMEKLQAIVSLRAAGYSQAVLRGWFDEAPGWMEDRIARHQAIRDELLHVLRGCEGVFARTPQAGSYLFPRLPKLAVAPAEFVKILRLQAGVVVTPGTEFSPHTADSVRLNFSQDHEAAVAAARRIVTLVERYRA 406
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------Aminotran_1_2-3nraB01 B:45-397                                                                                                                                                                                                                                                                                                                                   --------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------Aminotran_1_2-3nraB02 B:45-397                                                                                                                                                                                                                                                                                                                                   --------- Pfam domains (2)
         Sec.struct. author hhhhhhhh..---------....................ee.............hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh........eeeehhhhhhhhhhhhh......eeeeee...hhhhhhhhhh..eeeeee.............hhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhh.eeeee..............hhhhh...hhh.eeeee.......hhhhh.eeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.............ee.........hhhhhhhhhhhhhhee.ee.hhh.......eeee...hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nra B   2 SIEAKFKKLG---------RQSAAGLEALIRGAPIEGRPVDFSHGDVDAHEPTPGAFDLFSAGVQSGGVQAYTEYRGDLGIRDLLAPRLAAFTGAPVDARDGLIITPGTQGALFLAVAATVARGDKVAIVQPDYFANRKLVEFFEGEmVPVQLDYVSADETRAGLDLTGLEEAFKAGARVFLFSNPNNPAGVVYSAEEIGQIAALAARYGATVIADQLYSRLRYAGASYTHLRAEAAVDAENVVTImGPSkTESLSGYRLGVAFGSRAIIARmEKLQAIVSLRAAGYSQAVLRGWFDEAPGWmEDRIARHQAIRDELLHVLRGcEGVFARTPQAGSYLFPRLPKLAVAPAEFVKILRLQAGVVVTPGTEFSPHTADSVRLNFSQDHEAAVAAARRIVTLVERYRA 406
                                    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       341       351       361       371       381       391       401     
                                    11        21                                                                                                                             149-MSE                                                                                            248-MSE                   274-MSE                       304-MSE              325-CSD                                                                             
                                                                                                                                                                                                                                                                                    252-LLP
   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  (0, 0)

(no "SCOP Domain" information available for 3NRA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PLP_aminotran (240)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q3IWP3_RHOS4 | Q3IWP3)
molecular function
    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.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0008483    transaminase activity    Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.

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