1NX4 - JenaLib

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Title :   THE CRYSTAL STRUCTURE OF CARBAPENEM SYNTHASE (CARC)

Authors :   I. J. Clifton, L. X. Doan, M. C. Sleeman, M. Topf, H. Suzuki, R. C. Wilmout C. J. Schofield

Date :   08 Feb 03 (Deposition) - 17 Jun 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B,C  (2x)

Keywords :   Jelly Roll, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. J. Clifton, L. X. Doan, M. C. Sleeman, M. Topf, H. Suzuki, R. C. Wilmouth, C. J. Schofield
Crystal Structure Of Carbapenem Synthase (Carc).
J. Biol. Chem. V. 278 20843 2003
PubMed-ID: 12611886 | Reference-DOI: 10.1074/JBC.M213054200
(for further references see the PDB file header)

Molecule 1 - CARBAPENEM SYNTHASE
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET24A
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	CARC
	Organism Scientific	:	PECTOBACTERIUM CAROTOVORUM
	Organism Taxid	:	554
	Synonym	:	CARC

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (2x)	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 21)

No.	Name	Count	Type	Full Name
1	AKG	3	Ligand/Ion	2-OXOGLUTARIC ACID
2	FE	3	Ligand/Ion	FE (III) ION
3	MSE	15	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 36)

No.	Name	Count	Type	Full Name
1	AKG	6	Ligand/Ion	2-OXOGLUTARIC ACID
2	FE	-1	Ligand/Ion	FE (III) ION
3	MSE	30	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:101 , ASP A:103 , HIS A:251 , AKG A:280	BINDING SITE FOR RESIDUE FE A 300
2	AC2	SOFTWARE	HIS B:101 , ASP B:103 , HIS B:251 , AKG B:281 , HOH B:335	BINDING SITE FOR RESIDUE FE B 300
3	AC3	SOFTWARE	HIS C:101 , ASP C:103 , HIS C:251 , AKG C:282	BINDING SITE FOR RESIDUE FE C 300
4	AC4	SOFTWARE	LEU A:84 , VAL A:92 , HIS A:101 , ASP A:103 , THR A:130 , HIS A:251 , ARG A:253 , ARG A:263 , ARG A:267 , FE A:300	BINDING SITE FOR RESIDUE AKG A 280
5	AC5	SOFTWARE	LEU B:98 , HIS B:101 , ASP B:103 , THR B:130 , HIS B:251 , ARG B:253 , ARG B:263 , ARG B:267 , FE B:300 , HOH B:335	BINDING SITE FOR RESIDUE AKG B 281
6	AC6	SOFTWARE	HIS C:101 , ASP C:103 , THR C:130 , HIS C:251 , ARG C:253 , ARG C:263 , LEU C:265 , ARG C:267 , FE C:300	BINDING SITE FOR RESIDUE AKG C 282

(no "SS Bond" information available for 1NX4)

(no "Cis Peptide Bond" information available for 1NX4)

(no "SAP(SNP)/Variant" information available for 1NX4)

(no "PROSITE Motif" information available for 1NX4)

(no "Exon" information available for 1NX4)

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
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Chain A from PDB  Type:PROTEIN  Length:247
 aligned with CARC_PECCC | Q9XB59 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:271
                                    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 
           CARC_PECCC     2 SEIVKFNPVMASGFGAYIDHRDFLEAKTETIKNLLMRQGFVVVKNLDIDSDTFRDIYSAYGTIVEYADEKIGVGFGYRDTLKLEGEKGKIVTGRGQLPFHADGGLLLSQVDQVFLYAAEIKNVKFRGATTVCDHALACQEMPAHLLRVLEEETFEVRVLERGYYVDVSPDGWFKVPVFTDLGWVRKMLIYFPFDEGQPASWEPRIVGFTDHETQAFFQELGAFLKQPRYYYKHFWEDGDLLIMDNRRVIHEREEFNDDDIVRRLYRGQTAD 272
               SCOP domains d1nx4a_ A: Carbapenem synthase, CarC                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1nx4A00 A:2-272 Clavaminate synthase-like                                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............ee.hhhhhhhhhhhhhhhhhhhhheeee.....hhhhhhhhhhh..ee..------------...eee.............eeee...........eeeeeeeeee.......eeeeehhhhhhhhhhhhhhhhhhh.eeeee.------------.ee...eee....eee.............eeeee...hhhhhhhhhhhhhhhhh....eeee......eeeee...eeeee........eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nx4 A   2 SEIVKFNPVmASGFGAYIDHRDFLEAKTETIKNLLmRQGFVVVKNLDIDSDTFRDIYSAYGTIVE------------RDTLKLEGEKGKIVTGRGQLPFHADGGLLLSQVDQVFLYAAEIKNVKFRGATTVCDHALACQEmPAHLLRVLEEETFEVRVL------------WFKVPVFTDLGWVRKmLIYFPFDEGQPASWEPRIVGFTDHETQAFFQELGAFLKQPRYYYKHFWEDGDLLImDNRRVIHEREEFNDDDIVRRLYRGQTAD 272
                                    11        21        31     |  41        51        61    |    -       |81        91       101       111       121       131       141|      151        |-         - |     181      |191       201       211       221       231       241  |    251       261       271 
                                    11-MSE                    37-MSE                       66           79                                                            142-MSE           160          173            188-MSE                                                 244-MSE

Chain B from PDB  Type:PROTEIN  Length:256
 aligned with CARC_PECCC | Q9XB59 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:271
                                    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 
           CARC_PECCC     2 SEIVKFNPVMASGFGAYIDHRDFLEAKTETIKNLLMRQGFVVVKNLDIDSDTFRDIYSAYGTIVEYADEKIGVGFGYRDTLKLEGEKGKIVTGRGQLPFHADGGLLLSQVDQVFLYAAEIKNVKFRGATTVCDHALACQEMPAHLLRVLEEETFEVRVLERGYYVDVSPDGWFKVPVFTDLGWVRKMLIYFPFDEGQPASWEPRIVGFTDHETQAFFQELGAFLKQPRYYYKHFWEDGDLLIMDNRRVIHEREEFNDDDIVRRLYRGQTAD 272
               SCOP domains d1nx4b_ B: Carbapenem synthase, CarC                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1nx4B00 B:2-272 Clavaminate synthase-like                                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeehhhhhhhhhhhhhhhhhhhhheeee.....hhhhhhhhhhh..ee...-----.........eee.............eeee...........eeeeeeeeee.......eeeeehhhhhhhhhhhhhhhhhhh.eeeee.----------...ee...eee....eee.............eeeee...hhhhhhhhhhhhhhhhh....eeee......eeeee...eeeee........eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nx4 B   2 SEIVKFNPVmASGFGAYIDHRDFLEAKTETIKNLLmRQGFVVVKNLDIDSDTFRDIYSAYGTIVEY-----GVGFGYRDTLKLEGEKGKIVTGRGQLPFHADGGLLLSQVDQVFLYAAEIKNVKFRGATTVCDHALACQEmPAHLLRVLEEETFEVRVL----------DGWFKVPVFTDLGWVRKmLIYFPFDEGQPASWEPRIVGFTDHETQAFFQELGAFLKQPRYYYKHFWEDGDLLImDNRRVIHEREEFNDDDIVRRLYRGQTAD 272
                                    11        21        31     |  41        51        61     |   - |      81        91       101       111       121       131       141|      151        |-       171       181      |191       201       211       221       231       241  |    251       261       271 
                                    11-MSE                    37-MSE                        67    73                                                                  142-MSE           160        171              188-MSE                                                 244-MSE

Chain C from PDB  Type:PROTEIN  Length:250
 aligned with CARC_PECCC | Q9XB59 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:272
                                    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  
           CARC_PECCC     2 SEIVKFNPVMASGFGAYIDHRDFLEAKTETIKNLLMRQGFVVVKNLDIDSDTFRDIYSAYGTIVEYADEKIGVGFGYRDTLKLEGEKGKIVTGRGQLPFHADGGLLLSQVDQVFLYAAEIKNVKFRGATTVCDHALACQEMPAHLLRVLEEETFEVRVLERGYYVDVSPDGWFKVPVFTDLGWVRKMLIYFPFDEGQPASWEPRIVGFTDHETQAFFQELGAFLKQPRYYYKHFWEDGDLLIMDNRRVIHEREEFNDDDIVRRLYRGQTADI 273
               SCOP domains d1nx4c_ C: Carbapenem synthase, CarC                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1nx4C00 C:2-273 Clavaminate synthase-like                                                                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............ee.hhhhhhhhhhhhhhhhhhhhheeee.....hhhhhhhhhhhhhee....-----------..eee.............eeee...........eeeeeeeeee.......eeeeehhhhhhhhhhhhhhhhhhh.eeeee..-----------.ee...eee....eee.............eeeee...hhhhhhhhhhhhhhhhh....eeee......eeeee...eeeee........eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nx4 C   2 SEIVKFNPVmASGFGAYIDHRDFLEAKTETIKNLLmRQGFVVVKNLDIDSDTFRDIYSAYGTIVEYA-----------DTLKLEGEKGKIVTGRGQLPFHADGGLLLSQVDQVFLYAAEIKNVKFRGATTVCDHALACQEmPAHLLRVLEEETFEVRVLE-----------WFKVPVFTDLGWVRKmLIYFPFDEGQPASWEPRIVGFTDHETQAFFQELGAFLKQPRYYYKHFWEDGDLLImDNRRVIHEREEFNDDDIVRRLYRGQTADI 273
                                    11        21        31     |  41        51        61      |  -        81        91       101       111       121       131       141|      151       161         - |     181      |191       201       211       221       231       241  |    251       261       271  
                                    11-MSE                    37-MSE                         68          80                                                           142-MSE            161         173            188-MSE                                                 244-MSE

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: All beta proteins (24004)

Fold: Double-stranded beta-helix (580)

Superfamily: Clavaminate synthase-like (197)

Family: gamma-Butyrobetaine hydroxylase (5)

Protein domain: Carbapenem synthase, CarC (3)

Erwinia carotovora [TaxId: 554] (2)

1a	d1nx4a_	A:
1b	d1nx4b_	B:
1c	d1nx4c_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 4-Layer Sandwich (459)

Topology: Double-stranded beta-helix (19)

Homologous Superfamily: Clavaminate synthase-like (19)

Pectobacterium carotovorum. Organism_taxid: 554. (2)

1a	1nx4B00	B:2-272
1b	1nx4C00	C:2-273
1c	1nx4A00	A:2-272

(no "Pfam Domain" information available for 1NX4)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (CARC_PECCC | Q9XB59)

molecular function
	GO:0051213	dioxygenase activity	Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0017000	antibiotic biosynthetic process	The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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Biological Unit
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	1nx4
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	CARC_PECCC \| Q9XB59	:	1nx8 4oj8

1nx8	STRUCTURE OF CARBAPENEM SYNTHASE (CARC) COMPLEXED WITH N- ACETYL PROLINE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 21)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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